HLA-A2 Tumor Associated Antigen Peptides and Compositions

ABSTRACT

A peptide or composition comprising at least one HLA-A2 epi tope or analog from CEA, HER2/neu, MAGE2, MAGE3, or p53.

BACKGROUND OF THE INVENTION

1. Field of the Invention

This invention relates to the field of biology. In a particularembodiment, it relates to peptides, polynucleotides, and compositionsuseful to monitor or elicit an immune response to selectedtumor-associated antigens.

2. Related Art

The field of immunotherapy is yielding new approaches for the treatmentof, cancer, including the development of improved cancer vaccines (Krul,K. G., Decision Resources, 10.1-10.25 (1998)). While vaccines provide amechanism of directing immune responses towards the tumor cells, thereare a number of mechanisms by which tumor cells circumvent immunologicalprocesses (Pardoll, D. M., Nature Medicine (Vaccine Supplement),4:525-531 (1998)). Recent advances indicate that the efficacy of peptidevaccines may be increased when combined with approaches which enhancethe stimulation of immune responses, such as the use of Interleukin-2 orautologous dendritic cells (DC) (Abbas)et al., eds., Cellular andMolecular Immunology, 3^(rd) Edition, W. B. Saunders Company, pub.(1997)).

In a Phase I study, Murphy, et al., demonstrated that Human LeukocyteAntigen (HLA)-A2-binding peptides corresponding to sequences present inprostate specific antigen (PSA) stimulated specific cytotoxic T-celllymphocyte (CTL) responses in patients with prostate cancer (Murphy etal., The Prostate 29:371-380 (1996)). Rosenberg, et al., evaluated thesafety and mechanism of action of a synthetic HLA-A2 binding peptidederived from the melanoma associated antigen, gp100, as a cancer vaccineto treat patients with metastatic melanoma (Rosenberg et al., NatureMed., 4:321-327 (1998)). Based on immunological assays, 91% of patientswere successfully immunized with the synthetic peptide. In addition, 42%(13/31) of patients who received the peptide vaccine in combination withIL-2 treatment, demonstrated objective cancer responses. In addition,Nestle, et al., reported the vaccination of 16 melanoma patients withpeptide- or tumor lysate-pulsed DC (Nestle et al., Nature Med 4:328-332(1998)). Peptide-pulsed DC induced immune responses in 11/12 patientsimmunized with a vaccine comprised of 1-2 peptides. Objective responseswere evident in 5/16 (3 peptide-pulsed, 2 tumor-lysate pulsed) patientsevaluated in this study. These Phase I safety studies provided evidencethat HLA-A2 binding peptides of known tumor-associated antigensdemonstrate the expected mechanism of action. These vaccines weregenerally safe and well tolerated. Vaccine molecules related to atleaset four cancer antigens, CEA, HER2/neu, MAGE2, and, MAGE3 have beendisclosed. (Kawashima et al., Human Immunology, 59:1-14 (1998))

Preclinical studies have shown that vaccine-pulsed DC mediate anti-tumoreffects through the stimulation of antigen-specific CTL (Mandelboim etal., Nature Med., 1: 1179-1183 (1995); Celluzzi et al., J Exp Med183:283-287 (1996); Zitvogel et al., J Exp Med 183:87-97 (1996);Mayordomo et al., Nature Med 1:1297-1302 (1995)). CTL directly lysetumor cells and also secrete an array of cytokines such as interferongamma (IFNγ), tumor necrosis factor (TNF) and granulocyte-macrophagecolony stimulating factor (GM-CSF), that further amplify the immunereactivity against the tumor cells. CTL recognize tumor associatedantigens (TAA) in the form of a complex composed of 8-11 amino acidresidue peptide epitopes, bound to Major Histocompatibility Complex(MHC) molecules (Schwartz, B. D., The human major histocompatibilitycomplex HLA in basic & clinical immunology Stites et al., eds., LangeMedical Publication: Los Altos, pp. 52-64, 4^(th) ed.). Peptide epitopesare generated through intracellular processing of proteins. Theprocessed peptides bind to newly synthesized MHC molecules and theepitope-MHC complexes are expressed on the cell surface. Theseepitope-MHC complexes are recognized by the T cell receptor of the CTL.This recognition event is required for the activation of CTL as well asinduction of the effector functions such as lysis of the target tumorcell.

MHC molecules are highly polymorphic proteins that regulate T cellresponses (Schwartz, B. D., The human major histocompatibility complexHLA in basic & clinical immunology Stites et al., eds., Lange MedicalPublication: Los Altos, pp. 52-64, 4^(th) ed.). The species-specific MHChomologues that display CTL epitopes in humans are termed humanleukocyte antigen (“HLA”). HLA class I molecules can be divided intoseveral families or “supertypes” based upon their ability to bindsimilar repertoires of peptides. Vaccines which bind to multiple HLAsupertypes, such as for example A2, A3, and B7, will afford broad,non-ethnically biased population coverage. As seen in Table 1,population coverage is approximately 84-90% for various ethnicities,with an average coverage of the sample ethnicities at approximately 87%.

One of the main factors contributing to the dynamic interplay betweenhost and disease is the immune response mounted against the pathogen,infected cell, or malignant cell. In many conditions such immuneresponses control the disease. Several animal model systems andprospective studies of natural infection in humans suggest that immuneresponses against a pathogen can control the pathogen, preventprogression to severe disease and/or eliminate the pathogen. A commontheme is the requirement for a multispecific T cell response, and thatnarrowly focused responses appear to be less effective.

In the cancer setting there are several findings that indicate thatimmune responses can impact neoplastic growth:

First, the demonstration in many different animal models, thatanti-tumor T cells, restricted by MHC class I, can prevent or treattumors.

Second, encouraging results have come from immunotherapy trials.

Third, observations made in the course of natural disease correlated thetype and composition of T cell infiltrate within tumors with positiveclinical outcomes (Coulie P G, et al. Antitumor immunity at work in amelanoma patient In Advances in Cancer Research, 213-242, 1999).

Moreover, tumors commonly have the ability to mutate, thereby changingtheir immunological recognition. For example, the presence ofmonospecific CTL was also correlated with control of tumor growth, untilantigen loss emerged (Riker A, et al., Immune selection afterantigen-specific immunotherapy of melanoma Surgery, Aug: 126(2):112-20,1999; Marchand M, et al., Tumor regressions were observed in patientswith metastatic melanoma treated with an antigenic peptide derived fromthe MAGE-3 gene and presented by HLA-A1 Int. J. Cancer 80(2):219-30,Jan. 18, 1999). Similarly, loss of beta 2 microglobulin was detected in5/13 lines established from melanoma patients after receivingimmunotherapy at the National Cancer Institute (Restifo N P, et al.,Loss of functional Beta2-microglobulin in metastatic melanomas from fivepatients receiving immunotherapy Journal of the National CancerInstitute, Vol. 88 (2), 100-108, January 1996). It has long beenrecognized that HLA class I is frequently altered in various tumortypes. This deservation has led to a hypothesis that this phenomenonmight reflect immune pressure exerted on the tumor by means of class Irestricted CTL. The extent and degree of alteration in HLA class Iexpression appears to be reflective of past immune pressures, and mayalso have prognostic value (van Duinen S G, et al., Level of HLAantigens in locoregional metastases and clinical course of the diseasein patients with melanoma Cancer Research 48, 1019-1025, February 1988;Möller P, et ed., Influence of major histocompatibility complex class Iand II antigens on survival in colorectal carcinoma Cancer Research 51,729-736, January 1991). Taken together, these observations provide arationale for immunotherapy of cancer and infectious disease, andsuggest effective strategies that are needed to counteract the complexseries of pathological changes associated with disease.

The frequency of alterations in class I expression is the subject ofnumerous studies (Algarra I, et al., The HLA crossroad in tumorimmunology Human Immunology 61, 65-73, 2000). Rees and Mian estimateallelic loss to occur overall in 3-20% of tumors, and allelic deletionto occur in 15-50% of tumors. It should be noted that each cell carriestwo separate sets of class I genes, each gene carrying one HLA-A and oneHLA-B locus. Thus, fully heterozygous individuals carry two differentHLA-A molecules and two different HLA-B molecules. Accordingly, theactual frequency of losses for any specific allele could be as little asone quarter of the overall frequency. They also note that, in general, agradient of expression exists between normal cells, primary tumors andmetastatic tumors. In a study from Natali and coworkers (Natali P G, etal., Selective changes in expression of HLA class I. polymorphicdeterminants in human solid tumors PNAS USA 86:6719-6723, September1989), solid tumors were investigated for total HLA expression, usingthe W6/32 antibody, and for allele-specific expression of the A2antigen, as evaluated by use of the BB7.2-antibody. Tumor samples werederived from primary or metastatic tumors, for 13 different tumor types,and scored as “negative” if less than 20%, “reduced” if in the 30-80%range, and “normal” above 80%. All tumors, both primary and metastatic,were HLA positive with W6/32. In terms of A2 expression, a reduction wasnoted in 16.1% of the cases, and A2 was scored as undetectable in 39.4%of the cases. Gamido and coworkers (Gamido F, et al., Natural history ofHLA expression during tumour development Immunol Today 14(10):491-99,1993) emphasize that HLA changes appear to occur at a particular step inthe progression from benign to most aggressive. Jiminez et al (JiminezP, et al., Microsatellite instability analysis in tumors with differentmechanisms for total loss of BMA expression. Cancer Immunol Immunother48:684-90, 2000) have analyzed 118 different tumors (68 colorectal, 34laryngeal and 16 melanomas). The frequencies reported for total loss ofHLA expression were 11% for colon, 18% for melanoma and 13% for larynx.Thus, HLA class I expression is altered in a large fraction of the tumortypes, possibly as a reflection of immune pressure, or simply areflection of the accumulation of pathological changes and alterationsin diseased cells.

A majority of tumors express HLA class I, with a general tendency forthe more severe alterations to be found in later stage and lessdifferentiated tumors. This pattern is encouraging in the context ofimmunotherapy, especially considering that: 1) the relatively lowsensitivity of immunohistochemical techniques might underestimate HLAexpression in tumors; 2) class I expression can be induced in tumorcells as a result of local inflammation and lymphokine release; and, 3)class I negative cells are sensitive to lysis by NK cells.

Currently there are a number of unmet needs in the area of cancertreatment. This is evidenced by the side effects associated withexisting therapies employed for cancer treatment and the fact that lessthan 50% of patients are cured by current. therapies. Therefore, anopportunity exists for a product with the ability to either increaseresponse rates, duration of response, overall survival, disease freesurvival and/or quality of life.

SUMMARY OF THE INVENTION

In some embodiments, the invention is directed to an isolated peptidecomprising or consisting of one or more HLA-A2 epitopes and/or HLA-A2analogs. The peptide may comprise mutiple epitopes and/or analogs, andmay comprise additional amino acid residues, including but not limitedto, other CTL epitopes, universal HTL epitopes, HTL epitopes, linkers,spacers, carriers, etc.

In further embodiments, the invention is directed to polynucleotidesencoding such peptides.

In further embodiments, the invention is directed to a compositioncomprising two, three, four, five, six, seven, eight, nine, ten, elevenor twelve peptide epitopes and/or analogs. One or more of the peptidesand/or analogs in these embodiments may also further comprise additionalamino acid residues including, but not limited to, other CTL epitopes,HTL epitopes, universal HTL epitopes, linkers, spacers, carriers, etc.

In further embodiments, the invention is directed to a compositioncomprising one or more of the above peptides and/or polynucleotides andone or more additional components. Additional components includediluents, excipients, CTL epitopes, HTL epitopes, carriers, liposomes,HLA heavy chains, β2-microglobulin, strepavidin, antigen-presentingcells, adjuvants, etc.

In further embodiments, the invention is directed to prophylactic,therapeutic, diagnostic, and prognostic methods using the peptides,polynucleotides, and compositions of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS/FIGURES

FIG. 1 depicts that splenic DC from ProGP-treated mice induce CTLresponses in vivo. In FIG. 1, Splenic DC from ProGP treated HLA-A2.1transgenic mice (33 μg/mouse, QD, SC for 7 days) were pulsed in vitrowith HBV Pol 455 peptide (10⁶ cell per ml peptide at 10 μg/ml) inOpti-MEM I medium (Gibco Life Sciences) containing 3 μg/mlβ2-microglobulin (Scripps Laboratories). After peptide pulsing for 3 hrat room temperature, DC were washed twice and 10⁶ cells were injected IVinto groups of three transgenic mice. Epitope-pulsed GM-CSF/IL-4expanded DC and “mock-pulsed” ProGP derived DC were also tested forcomparison. Seven days after receiving the primary immunization with DC,animals were boosted with the same DC populations. At fourteen daysafter the primary immunization, spleen cells from immunized animals wererestimulated twice in vitro in the presence of the Pol 455 peptide. CTLactivity following restimulations was measured using a standard ⁵¹Crrelease assay in which the lysis of ⁵¹Cr-labeled HLA-A2.1-transfectedJurkat target cells was measured in the presence (circle symbols) orabsence of peptide (square symbols). The data points shown in Panels A-Crepresent a composite of lytic activity from a triplicate set ofcultures. Panel A, splenic DC from ProGP(SD-9427) treated animals pulsedwith the HBV Pol 455 peptide. Panel B, GM-CSF/IL-4 expanded DC pulsedwith HBV Pol 455 peptide. Panel C, mock-pulsed DC from ProGP treatedanimals. Studies were performed at Epimmune Inc., San Diego, Calif.

FIG. 2 presents a schematic of a dendritic cell pulsing and testingprocedure.

FIG. 3A shows a flow chart of the preparation of Drug Product.

FIG. 3B shows multi-epitope CTL induction in HLA-A2.1/K^(b) transgenicmice immunized with the EP-2101 vaccine. Mice were immunized with 50 μgof EP-2101 (10 mg/ml emulsion dose) or co-immunized with 50 μg of eachCTL epitope individually with an equal dose of PADRE® epitope inMontanide® ISA 51 adjuvant (latter responses designated as“Individual”). Eleven to 14 days later, splenocytes from primed animalswere stimulated with each CTL peptide in vitro and six days later CTLactivity from triplicate cultures were measured with an in situ IFN-γELISA. As a control, splenocytes from naïve mice or mice injected with aMontanide® ISA 51 emulsion prepared without peptide were also stimulatedwith peptide in vitro and CTL activity was measured under identicalconditions (responses designated as “Naïve control”). Data shown foreach epitope is the geometric mean CTL response from 6-10 independentexperiments. CTL responses are expressed in secretory units (SU) with 1SU defined as the release of 100 pg/well of IFN-γ by 10⁶ effector cells.

DETAILED DESCRIPTION OF THE INVENTION

This invention provides peptides that can be used to monitor an immuneresponse to a tumor associated antigen or to create a cancer vaccinethat stimulates the cellular arm of the immune system, especially whenone or more peptides are combined. In particular embodiments,compositions mediate immune responses against tumors in individuals whobear at least one allele of HLA-A2 and/or HLA-A2 supertype. Suchcompositions will generally be referred to as A2 compositions (orcombinations thereof).

An A2 composition may, for example, act as a vaccine to stimulate theimmune system to recognize and kill tumor cells, leading to increasedquality of life, and/or disease-free or overall survival rates forpatients treated for cancer. In a preferred embodiment, a composition ofthe invention such as a vaccine will be administered to HLA-A2 or HLA-A2supertype positive individuals who have a cancer that expresses at leastone of the TAAs from which the epitopes or analogs were selected (e.g.,CEA, p53, HER2/neu, MAGE2/3), examples of such cancers being breast,colon, lung, ovarian and gastric cancers and for MAGE 2/3, somemelanomas. Thereby, an A2 compostion, e.g., vaccine, improves thestandard of care for patients being treated for breast, colon, lung,ovarian or gastric cancers, or melanoma.

A2 compositions, e.g., vaccines, of the invention comprise peptidesbearing A2 motifs or A2 supermotifs (A2 epitopes and/or A2 analogs), asdescribed herein, and/or nucleic acids encoding such peptides. Suchcompositions may also comprise a PADRE® epitope.

The peptides and corresponding nucleic acids and compositions of thepresent invention are useful for stimulating an immune response to TAAsby stimulating the production of CTL and optionally HTL responses, e.g.therapeutic prophylaxis, and are also useful for monitoring an immuneresponse, e.g., diagnosis and prognosis. The peptides, which contain A2epitopes derived directly or indirectly (i.e. by analoging) from nativeTAA protein amino acid sequences, are able to bind to HLA molecules andstimulate an immune response to TAAs. The complete sequence of the TAAsproteins analyzed described as SEQ ID NOs:11-15 herein can be obtainedfrom GenBank. See Table 2.

The epitopes of the invention have been identified in a number of ways,as will be discussed below. Also discussed in greater detail is anembodiment of the invention in which analogs have been derived whereinthe binding activity for HLA molecules or T cell receptor molecules wasmodulated by modifying specific amino acid residues to create analogswhich exhibit altered (e.g., improved) immunogenicity.

DEFINITIONS

The invention can be better understood with reference to the followingdefinitions:

Throughout this disclosure, “binding data” results are often expressedin terms of “IC₅₀'s.” IC₅₀ is the concentration of peptide in a bindingassay at which 50% inhibition of binding of a reference peptide isobserved. Given the conditions in which the assays are run (i.e.,limiting HLA proteins and labeled peptide concentrations), these valuesapproximate K_(D) values. Assays for determining binding are describedin detail, e.g., in PCT publications WO 94/20127 and WO 94/03205, andother publications such Sidney et al., Current Protocols in Immunology18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); and Sette, etal., Mol. Immunol. 31:813 (1994). It should be noted that IC₅₀ valuescan change, often dramatically, if the assay conditions are varied, anddepending on the particular reagents used (e.g., HLA preparation, etc.).For example, excessive concentrations of HLA molecules will increase theapparent measured IC₅₀ of a given ligand.

Alternatively, binding is expressed relative to a reference peptide.Although as a particular assay becomes more, or less, sensitive, theIC₅₀'s of the peptides tested may change somewhat, the binding relativeto the reference peptide will not significantly change. For example, inan assay run under conditions such that the IC₅₀ of the referencepeptide increases 10-fold, the IC₅₀ values of the test peptides willalso shift approximately 10-fold. Therefore, to avoid ambiguities, theassessment of whether a peptide is a good (i.e. high), intermediate,weak, or negative binder is generally based on its IC₅₀, relative to theIC₅₀ of a standard peptide. The Tables included in this applicationpresent binding data in a preferred biologically relevant form of IC₅₀nM.

Binding may also be determined using other assay systems including thoseusing: live cells (e.g., Ceppellini et al., Nature 339:392 (1989);Christnick et al., Nature 352:67 (1991); Busch et al., Int. Immunol2:443 (1990); Hill et al., J. Immunol. 147:189 (1991); del Guercio etal., J. Immunol. 154:685 (1995)), cell free systems using detergentlysates (e.g., Cerundolo et al., J. Immunol. 21:2069 (1991)),immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890(1994); Marshall et al., J. Immunol. 152:4946 (1994)), ELISA systems(e.g., Reay et al., EMBO J. 11:2829 (1992)), surface plasmon resonance(e.g., Khilko et al., J. Biol. Chem. 268:15425 (1993)); high fluxsoluble phase assays (Hammer et al., J. Exp. Med. 180:2353 (1994)), andmeasurement of class I MHC stabilization or assembly (e.g., Ljunggren etal., Nature 346:476 (1990); Schumacher; et al., Cell 62:563 (1990);Townsend et al., Cell 62:285 (1990); Parker et al., J. Immunol. 149:1896(1992)).

As used herein, “high affinity” with respect to HLA class I molecules isdefined as binding with an IC₅₀ or K_(D) value, of 50 nM or less,“intermediate affinity” is binding with an IC₅₀ or K_(D) value ofbetween 50 and about 500 nM, “weak affinity” is binding with an IC₅₀ orK_(D) value of between about 500 and about 5000 nM. “High affinity” withrespect to binding to HLA class II molecules is defined as binding withan IC₅₀ or K_(D) value of 100 nM or less; “intermediate affinity” isbinding with an IC_(so) or K_(D) value of between about 100 and about1000 nM.

A “computer” or “computer system” generally includes: a processor andrelated computer programs; at least one information storage/retrievalapparatus such as a hard drive, a disk drive or a tape drive; at leastone input apparatus such as a keyboard, a mouse, a touch screen, or amicrophone; and display structure, such as a screen or a printer.Additionally, the computer may include a communication channel incommunication with a network. Such a computer may include more or lessthan what is listed above.

“Cross-reactive binding” indicates that a peptide is bound by more thanone HLA molecule; a synonym is degenerate binding.

The term “derived” when used to discuss an epitope is a synonym for“prepared.” A derived epitope can be isolated from a natural source, orit can be synthesized in accordance with standard protocols in the art.Synthetic epitopes can comprise artificial amino acid residues “aminoacid mimetics,” such as D isomers of natural occurring L amino acidresidues or non-natural amino acid residues such as cyclohexylalanine. Aderived or prepared epitope can be an analog of a native epitope.

A “diluent” includes sterile liquids, such as water and oils, includingthose of petroleum, animal, vegetable or synthetic origin, such aspeanut oil, soybean oil, mineral oil, sesame oil and the like. Water isa preferred diluent for pharmaceutical compositions. Saline solutionsand aqueous dextrose and glycerol solutions can also be employed asdiluents, particularly for injectable solutions.

A “dominant epitope” is an epitope that induces an immune response uponimmunization with a whole native antigen (see, e.g., Sercarz, et al.,Annu. Rev. Immunol. 11:729-766, 1993). Such a response is cross-reactivein vitro with an isolated peptide epitope.

An “epitope” is the collective features of a molecule, such as primary,secondary and tertiary peptide structure, and charge, that together forma site recognized by an immunoglobulin, T cell receptor or HLA molecule.Alternatively, an epitope can be defined as a set of amino acid.residues which is involved in recognition by a particularimmunoglobulin, or in the context of T cells, those residues necessaryfor recognition by T cell receptor proteins and/or MajorHistocompatibility Complex (MHC) receptors. Epitopes are present innature, and can be isolated, purified or otherwise prepared or derivedby humans. For example, epitopes can be prepared by isolation from anatural source, or they can be synthesized in accordance with standardprotocols in the art. Synthetic epitopes can comprise artificial aminoacid residues, “amino acid mimetics,” such as D isomers ofnaturally-occurring L amino acid residues or non-naturally-occurringamino acid residues such as cyclohexylalanine. Throughout thisdisclosure, epitopes may be referred to in some cases as peptides orpeptide epitopes. The epitopes and analogs of the invention are setforth in Table 3.

It is to be appreciated that proteins or peptides that comprise anepitope or an analog of the invention as well as additional aminoacid(s) are still within the bounds of the invention. In certainembodiments, the peptide comprises a fragment of an antigen. A “fragmentof an antigen” or “antigenic fragment” or simply “fragment” is a portionof an antigen which has 100% identity with a wild type antigen ornaturally-ocurring variant thereof. The fragment may or may not comprisean epitope of the invention. The fragment may be less than or equal to600 amino acid residues, less than or equal to 500 amino acid residues,less than or equal to 400 amino acid residues, less than or equal to 250amino acid residues, less than or equal to 100 amino acid residues, lessthan or equal to 85 amino acid residues, less than or equal to 75 aminoacid residues, less than or equal to 65 amino acid residues, or lessthan or equal to 50 amino acid residues in length. In certainembodiments, a fragment is e.g., less than 101 or less than 51 aminoacid residues in length, in any increment down to 5 amino acid residuesin length. For example, the fragment may be 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 aminoacid residues in length. In preferred embodiments, a peptide is 9, 10,or 11 amino acid residues in length.

In certain embodiments, there is a limitation on the length of a peptideof the invention. The embodiment that is length-limited occurs when theprotein or peptide comprising an epitope of the invention comprises aregion (i.e., a contiguous series of amino acid residues) having 100%identity with a native sequence. In order to avoid the definition ofepitope from reading, e.g., on whole natural molecules, there is alimitation on the length of any region that has 100% identity with anative peptide sequence. Thus, for a peptide comprising an epitope ofthe invention and a region with 100% identity with a native peptidesequence, the region with 100% identity to a native sequence generallyhas a length of: less than or equal to 600 amino acid residues, oftenless than or equal to 500 amino acid residues, often less than or equalto 400 amino acid residues, often less than or equal to 250 amino acidresidues, often less than or equal to 100 amino acid residues, oftenless than or equal to 85 amino acid residues, often less than or equalto 75 amino acid residues, often less than or equal to 65 amino acidresidues, and often less than or equal to 50 amino acid residues. Incertain embodiments, an “epitope” of the invention is comprised by apeptide having a region with less than 51 amino acid residues that has100% identity to a native peptide sequence, in any increment down to 5amino acid residues; for example 50, 49, 48, 47, 46, 45, 44, 43, 42, 41,40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23,22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3,2 or 1 amino acid residues.

Accordingly, peptide or protein sequences longer than 600 amino acidresidues are within the scope of the invention, provided that they donot comprise any contiguous sequence of more than 600 amino acidresidues that have 100% identity with a native peptide sequence. For anypeptide that has five contiguous residues or less that correspond to anative sequence, there is no limitation on the maximal length of thatpeptide in order to fall within the scope of the invention. It ispresently preferred that a peptide of the invention (e.g., a peptidecomprising an epitope of the invention) be less than 600 residues longin any increment down to eight amino acid residues. In a preferredembodiment, peptides of the invention are 9, 10 or 11 amino acidresidues in length.

“Human Leukocyte Antigen” or “HLA” is a human class I or class II MajorHistocompatibility Complex (MHC) protein (see, e.g., Stites, et al.,IMMUNOLOGY, 8^(TH) ED., Lange Publishing, Los Altos, Calif. (1994).

An “HLA supertype or HLA family”, as used herein, describes sets of HLAmolecules grouped on the basis of shared peptide-binding specificities.HLA class I molecules that share somewhat similar binding affinity forpeptides bearing certain amino acid motifs are grouped into such HLAsupertypes. The terms HLA superfamily, HLA supertype family, HLA family,and HLA xx-like molecules (where “xx” denotes a particular HLA type),are synonyms. See, e.g., the HLA-A2 motif and super motifs are detailedin Tables 4A, 4B, 4C, and 4D.

As used herein, “high affinity” with respect to HLA class I molecules isdefined as binding with an IC₅₀, or K_(D) value, of 50 nM or less;“intermediate affinity” is binding with an IC₅₀ or K_(D) value ofbetween about 50 and about 500 nM; “weak affinity” is binding with anIC₅₀ or K_(D) value between about 500 and about 5000 nM. “High affinity”with respect to binding to HLA class II molecules is defined as bindingwith an IC₅₀ or K_(D) value of 100 nM or less; “intermediate affinity”is binding with an IC₅₀ or K_(D) value of between about 100 and about1000 nM. See “binding data.”

An “IC₅₀” is the concentration of peptide in a binding assay at which50% inhibition of binding of a reference peptide is observed. Given theconditions in which the assays are run (i.e., limiting HLA proteins andlabeled peptide concentrations), these values approximate K_(D) values.See “binding data.”

The terms “identical” or percent “identity,” in, the context of two ormore peptide sequences or antigen fragments, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues that are the same, when compared andaligned for maximum correspondence over a comparison window, as measuredusing a sequence comparison algorithm or by manual alignment and visualinspection.

An “immunogenic” peptide or an “immunogenic” epitope or “peptideepitope” is a peptide that comprises an allele-specific motif orsupermotif such that the peptide will bind an HLA molecule and induce aCTL and/or HTL response. Thus, immunogenic peptides of the invention arecapable of binding to an appropriate HLA molecule and thereafterinducing a cytotoxic T lymphocyte (CTL) response, or a helper Tlymphocyte (HTL) response, to the peptide.

The phrases “isolated” or “biologically pure” refer to material which issubstantially or essentially free from components which normallyaccompany the material as it is found in its native state. Thus,isolated peptides in accordance with the invention preferably do notcontain materials normally associated with the peptides in their in situenvironment. An “isolated” epitope refers to an epitope that does notinclude the whole sequence of the antigen from which the epitope wasderived. Typically the “isolated” epitope does not have attached theretoadditional amino acid residues that result in a sequence that has 100%identity over the entire length of a native sequence. The nativesequence can be a sequence such as a tumor-associated antigen from whichthe epitope is derived. Thus, the term “isolated” means that thematerial is removed from its original environment (e.g., the naturalenvironment if it is naturally occurring). For example, anaturally-occurring polynucleotide or peptide present in a living animalis not isolated, but the same polynucleotide or peptide, separated fromsome or all of the coexisting materials in the natural system, isisolated. Such a polynucleotide could be part of a vector, and/or such apolynucleotide or peptide could be part of a composition, and still be“isolated” in that such vector or composition is not part of its naturalenvironment. Isolated RNA molecules include in vivo or in vitro RNAtranscripts of the DNA molecules of the present invention, and furtherinclude such molecules produced synthetically.

“Major Histocompatibility Complex” or “MHC” is a cluster of genes thatplays a role in control of the cellular interactions responsible forphysiologic immune responses. In humans, the MHC complex is also knownas the human leukocyte antigen (HLA) complex. For a detailed descriptionof the MHC and HLA complexes, see, Paul, FUNDAMENTAL IMMUNOLOGY, 3′ ED.,Raven Press, New York (1993).

A “native” or a “wild type” sequence refers to a sequence found innature. Such a sequence may comprise a longer sequence in nature.

A “negative binding residue” or “deleterious residue” is an amino acidresidue which, if present at certain positions (typically not primaryanchor positions) in a peptide epitope, results in decreased bindingaffinity of the peptide for its corresponding HLA molecule.

The terms “peptide” and “peptide epitope” are used interchangeably with“oligopeptide” in the present specification to designate a series ofresidues, typically L-amino acid residues, connected one to the other,typically by peptide bonds between the α-amino and carboxyl groups ofadjacent amino acid residues.

“Synthetic peptide” refers to a peptide that is abtained from anon-natural source, e.g., is man-made. Such peptides may be producedusing such methods as chemical synthesis or recombinant DNA technology.“Synthetic peptides” include “fusion proteins.”

A “PanDR binding” peptide, a “PanDR binding epitope,” or “PADRE®”peptide (Epimmune, San Diego, Calif.) is a member of a family ofmolecules that binds more than one HLA class II DR molecule. The patternthat defines the PADRE® family of molecules can be referred to as an HLAClass II supermotif. A PADRE® molecule binds to HLA-DR molecules andstimulates in vitro and in vivo human helper T lymphocyte (HTL)responses. For a further definition of the PADRE® family, see copendingapplication U.S. Ser. No. 09/709,774, filed Nov. 11, 2000; and09/707,738, filed Nov. 6, 2000; PCT publication Nos WO 95/07707, and WO97/26784; U.S. Pat. Nos. 5,736,142 issued Apr. 7, 1998; 5,679,640,issued Oct. 21, 1997; and 6,413,935, issued Jul. 2, 2002.

“Pharmaceutically acceptable” refers to a generally non-toxic, inert,and/or physiologically compatible composition or component of acomposition.

A “pharmaceutical excipient” or “excipient” comprises a material such asan adjuvant, a carrier, pH-adjusting and buffering agents, tonicityadjusting agents, wetting agents, preservatives, and the like. A“pharmaceutical excipient” is an excipient which is pharmaceuticallyacceptable.

The term “motif” refers to a pattern of residues in an amino acidsequence of defined length, preferably a peptide of less than about 15ammo acid residues in length, or less than about 13 amino acid residuesin length, usually from about 8 to about 13 amino acid residues (e.g.,8, 9, 10, 11, 12, or 13) for a class I HLA motif and from about 6 toabout 25 amino acid residues (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) for a class U HLA motif,which is recognized by a particular HLA molecule. Motifs are typicallydifferent for each HLA protein encoded by a given human HLA allele.These motifs often differ in their pattern of the primary and secondaryanchor residues. In preferred embodiments, an MHC class I motifidentifies a peptide of 9, 10, Or 11 amino acid residues in length.

A “supermotif” is a peptide binding specificity shared by HLA moleculesencoded by two or more HLA alleles. Preferably, a supermotif-bearingpeptide is recognized with high or intermediate affinity (as definedherein) by two or more HLA antigens.

A “primary anchor residue” is an amino acid at a specific position alonga peptide sequence which is understood to provide a primary contactpoint between the immunogenic peptide and the HLA molecule. One, two orthree, primary anchor residues within a peptide of defined lengthminimally defines a “motif” for an immunogenic peptide. These residuesare understood to fit in close contact with peptide binding grooves ofan HLA molecule, with their side chains buried in specific pockets ofthe binding grooves themselves. In one embodiment of an HLA class Imotif, the primary anchor residues are located at position 2 (from theamino terminal position) and at the carboxyl terminal position of apeptide epitope in accordance with the invention. The primary anchorpositions for the A2 motif and supermotif of HLA Class I are set forthin Tables 4A, 4B, 4C, and 4D. For example, analog peptides can becreated by altering the presence or absence of particular residues inthese anchor positions. Such analogs are used to modulate the bindingaffinity of an epitope comprising a particular motif or supermotif.

A “secondary anchor residue” is an amino acid at a position other than aprimary anchor position in a peptide which may influence peptidebinding. A secondary anchor residue occurs at a significantly higherfrequency among HLA-bound peptides than would be expected by randomdistribution of amino acid residues at a given position. A secondaryanchor residue can be identified as a residue which is present at ahigher frequency among high or intermediate affinity binding peptides,or a residue otherwise associated with high or intermediate affinitybinding. The secondary anchor residues are said to occur at “secondaryanchor positions.” For example, analog peptides can be created byaltering the presence or absence of particular residues in thesesecondary anchor positions. Such analogs are used to finely modulate thebinding affinity of an epitope comprising a particular motif orsupermotif. The terminology “fixed peptide” is generally used to referto an analog peptide that has changes in primary anchore position; notsecondary. A “cryptic epitope” elicits a response by immunization withan isolated peptide, but the response is not cross-reactive in vitrowhen intact whole protein, which comprises the epitope, is used as anantigen.

“Promiscuous recognition” by a TCR is where a distinct peptide isrecognized by various T cell clones in the context of various HLAmolecules. Promiscuous binding by an HLA molecule is synonymous withcross-reactive binding.

A “protective immune response” or “therapeutic immune response” refersto a CTL and/or an HTL response to an antigen derived from an pathogenicantigen (e.g., an antigen from an infectious agent or a tumor antigen),which in some way prevents or at least partially arrests diseasesymptoms, side effects or progression. The immune response may alsoinclude an antibody response which has been facilitated by thestimulation of helper T cells.

The term “residue” refers to an amino acid residue or amino acid mimeticresidue incorporated into a peptide or protein by an amide bond or amidebond mimetic.

A “subdominant epitope” is an epitope which evokes little or no responseupon immunization with a whole antigen or a fragment of the wholeantigen comprising a subdominant epitope and a dominant epitope, whichcomprise the epitope, but for which a response can be obtained byimmunization with an isolated peptide, and this response (unlike thecase of cryptic epitopes) is detected when whole antigen or a fragmentof the whole antigen comprising a subdominant epitope and a dominantepitope is used to recall the response in vitro or in vivo.

As used herein, a “vaccine” is a composition used for vaccination, e.g.,for prophylaxis or therapy, that comprises one or more peptides of theinvention. There are numerous embodiments of vaccines in accordance withthe invention, such as by a cocktail of one or more peptides; one ormore peptides of the invention comprised by a polyepitopic peptide; ornucleic acids that encode such peptides or polypeptides, e.g., aminigene that encodes a polyepitopic peptide. The “one or more peptides”can include any whole unit integer from 1-150, e.g., at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130,135, 140, 145, or 150 or more peptides of the invention. The peptides orpolypeptides can optionally be modified, such as by lipidation, additionof targeting or other sequences. HLA class I-binding peptides of theinvention can be linked or to otherwise be combined with HLA classII-binding peptides, e.g., a PADRE® universal HTL-bindind peptide, tofacilitate activation of both cytotoxic T lymphocytes and helper Tlymphocytes. Vaccines can comprise peptide pulsed antigen presentingcells, e.g., dendritic cells.

The nomenclature used to describe peptides or proteins follows theconventional practice wherein the amino group is presented to the left(the amino- or N-terminus) and the carboxyl group to the right (thecarboxy- or C-terminus) of each amino acid residue. When amino acidresidue positions are referred to in a peptide epitope they are numberedin an amino to carboxyl direction with position one being the residuelocated at the amino terminal end of the epitope, or the peptide orprotein of which it may be a part.

In the formulae representing selected specific embodiments of thepresent invention, the amino- and carboxyl-terminal groups, although notspecifically shown, are in the form they would assume at physiologic pHvalues, unless otherwise specified. In the amino acid structureformulae, each residue is generally represented by standard three letteror single letter designations. The L-form of an amino acid residue isrepresented by a capital single letter or a capital first letter of athree-letter symbol, and the D-form for those amino acid residues havingD-forms is represented by a lower case single letter or a lower casethree letter symbol. However, when three letter symbols or full namesare used without capitals, they may refer to L amino acid residues.Glycine has no asymmetric carbon atom and is simply referred to as “Gly”or “G”. The amino acid sequences, of peptides set forth herein aregenerally designated using the standard single letter symbol. (A,Alanine; C, Cysteine; D, Aspartic Acid; E, Glutamic Acid; F,Phenylalanine; G, Glycine; H, Histidine; I, Isoleucine; K, Lysine; L,Leucine; M, Methionine; N, Asparagine; P, Proline; Q, Glutamine; R,Arginine; S, Serine; T, Threonine; V, Valine; W, Tryptophan; and Y,Tyrosine.) In addition to these symbols, “B” in the single letterabbreviations used herein designates α-amino butyric acid. In someembodiments, α-amino butyric acid may be interchanged with cysteine.

-   -   Acronyms used herein are as follows:

-   APC: Antigen presenting cell

-   CD3: Pan T cell marker

-   CD4: Helper T lymphocyte marker

-   CD8: Cytotoxic T lymphocyte marker

-   CEA: Carcinoembryonic antigen (see, e.g., SEQ ID NO: 363)

-   CTL: Cytotoxic T lymphocyte

-   DC: Dendritic cells. DC function as potent antigen presenting cells    by stimulating cytokine release from CTL lines that are specific for    a model peptide derived from hepatitis B virus. In vivo experiments    using DC pulsed ex vivo with an HBV peptide epitope have stimulated    CTL immune responses in vivo following delivery to naïve mice.

-   DLT: Dose-limiting toxicity, an adverse event related to therapy.

-   DMSO: Dimethylsulfoxide

-   ELISA: Enzyme-linked immunosorbant assay

-   E:T: Effector:Target ratio

-   G-CSF: Granulocyte colony-stimulating factor

-   GM-CSF: Granulocyte-macrophage (monocyte)-colony stimulating factor

-   HBV: Hepatitis B virus

-   HER2/neu: A tumor associated antigen; c-erbB-2 is a synonym (see,    e.g., SEQ ID NO: 364)

-   HLA: Human leukocyte antigen

-   HLA-DR: Human leukocyte antigen class II

-   HPLC: High Performance Liquid Chromatography

-   HTC: Helper T Cell

-   HTL: Helper T Lymphocyte. A synonym for HTC.

-   ID: Identity

-   IFNγ: Interferon gamma

-   IL-4: Interleukin-4

-   Intravenous

-   LU_(30%): Cytotoxic activity for 10⁶ effector cells required to    achieve 30% lysis of a target cell population, at a 100:1 (E:T)    ratio.

-   MAb: Monoclonal antibody

-   MAGE: Melanoma antigen (see, e.g., SEQ ID NO: 365 and 366 for MAGE2    and MAGE3, respectively)

-   MLR: Mixed lymphocyte reaction

-   MNC: Mononuclear cells

-   PB: Peripheral blood

-   PBMC: Peripheral blood mononuclear cell

-   ProGP: Progenipoietin product (Searle, St. Louis, Mo.), a chimeric    flt3/G-CSF receptor agonist.

-   SC: Subcutaneous

-   S.E.M.: Standard error of the mean

-   QD: Once a day dosing

-   TAA: Tumor Associated Antigen

-   TNF: Tumor necrosis factor

-   WBC: White blood cells

The following describes the peptides, corresponding nucleic acidmolecules, compositions, and methods of the invention in more detail.

A2 Peptides and Polynucleotides of Tumor Associated Antigens

A2 Epitopes and Analogs. In some embodiments, the invention is directedto an isolated peptide comprising or consisting of an epitope and/oranalog. In some embodiments, the invention is directed to an isolatedpolynucleotide encoding such a peptide.

The isolated epitopes and analogs of the invention are all class Ibinding peptides, i.e., CTL peptides. In particular, the epitopes andanalogs of the invention comprise an A2 motif or supermotif. Epitopesand analogs of the invention are those set forth in Table 3 (SEQ IDNOs:1-10). A2 epitopes and analogs of the invention may be referred toherein as “epitopes” and “analogs” or referred to by Table or referredto by SEQ ID NO. Other epitopes and analogs are referred to herein asCTL epitopes or CTL peptides and HTL epitopes or HTL peptides.

Peptides and Polynucleotides. In some embodiments, the invention isdirected to an isolated peptide comprising or consisting of an epitopeand/or analog, wherein the epitope or analog consists of a sequenceselected from those in Table 3 (SEQ ID NOs:1-10).

Preferably, the peptide comprises or consists of an epitope or analogconsisting of a sequence in Table 3.

Peptides of the invention may be fusion proteins of epitope(s) and/oranalog(s) to CTL epitope(s), and/or HTL epitope(s), and/or linker(s),and/or spacer(s), and/or carrier(s), and/or additional amino acidresidue(s), and/or may comprise or consist of homopolymers of an epitopeor analog or heteropolymers of epitopes and/or analogs, as is describedin detail below.

Peptides which comprise an epitope and/or analog of the invention maycomprise or consist of a fragment of an antigen (“fragment” or“antigenic fragment”), wherein the fragment comprises an epitope and/oranalog. The fragment may be a portion of CEA, HER2/neu MAGE2, MAGE3,and/or p53 (SEQ ID Nos:11, 12, 13, 14, and 15, respectively). Theepitope of the invention may be within the fragment or may be linkeddirectly or indirectly, or otherwise connected to the fragment.

The fragment may comprise or consist of a region of a native antigenthat contains a high concentration of class I and/or class II epitopes,preferably it contains the greatest number of epitopes per amino acidlength. Such epitopes can be present in a frame-shifted manner, e.g., a10 amino acid long peptide could contain two 9 amino acid residue longepitopes and one 10 amino acid residue long epitope.

The fragment may be less than or equal to 600 amino acid residues, lessthan or equal to 500 amino acid residues, less than or equal to 400amino acid residues, less than or equal to 250 amino acid residues, lessthan or equal to 100 amino acid residues, less than or equal to 85 aminoacid residues, less than or equal to 75 amino acid residues, less thanor equal to 65 amino acid residues, or less than or equal to 50 aminoacid residues in length. In certain embodiments, a fragment is less than101 amino acid residues in length, in any increment down to 5 amino acidresidues in length. For example, the fragment may be 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82,83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or100 amino acid residues in length. In preferred embodiments, fragmentsare 9, 10, or 11 amino acid residues in length.

Fragments of the full length CEA antigen may be fragments from aboutresidue 1-20, 21-40, 41-60, 61-80, 81-100, 101-120, 121-140, 141-160,161-180, 181-200, 201-220, 221-240, 241-260, 261-280, 281-300, 301-320,321-340, 341-360, 361-380, 381-400, 401-420, 421-440, 441-460, 461-480,481-500, 501-520, 521-540, 541-560, 561-580, 581-600, 601-620, 621-640,641-660, 661-680 or 681 to the C-terminus of the antigen.

Fragments of the full length HER2/neu antigen may be fragments fromabout residue 1-20, 21-40, 41-60, 61-80, 81-100, 101-120, 121-140,141-160, 161-180, 181-200, 201-220, 221-240, 241-260, 261-280, 281-300,301-320, 321-340, 341-360, 361-380, 381-400, 401-420, 421-440, 441-460,461-480, 481-500, 501-520, 521-540, 541-560, 561-580, 581-600, 601-620,621-640, 641-660, 661-680, 681-700, 701-720, 721-740, 741-760, 761-780,781-800, 801-820, 821-840, 841-860, 861-880, 881-900, 901-920, 921-940,941-960, 961-980, 981-1000, 1001-1020, 1021-1040, 1041-1060, 1061-1080,1081-1100, 1101-1120, 1121-1140, 1141-1160, 1161-1180, 1181-1200,1201-1220, 1221-1240, or 1241 to the C-terminus of the antigen.

Fragments of the full length MAGE-2 antigen' may be fragments from aboutresidue 1-20, 21-40, 41-60, 61-80, 81-100, 101-120, 121-140, 141-160,161-180, 181-200, 201-220, 221-240, 241-260, 261-280, 281-300 or 301 tothe C-terminus of the antigen.

Fragments of the full length MAGE-3 antigen may be fragments from aboutresidue 1-20, 21-40, 41-60, 61-80, 81-100, 101-120, 121-140, 141-160,161-180, 181-200, 201-220, 221-240, 241-260, 261-280, 281-300 or 301 tothe C-terminus of the antigen.

Fragments of the full length p53 antigen may be fragments from aboutresidue 1-20, 21-40, 41-60, 61-80, 81-100, 101-120, 121-140, 141-160,161-180, 181-200, 201-220, 221-240, 241-260, 261-280, 281-300, 301-320,321-340, 341-360, 361-380 or 381 to the C-terminus of the antigen.

Peptides which comprise an epitope and/or analog of the invention may bea fusion protein comprising one or more amino acid residues in additionto the epitope, analog, or fragment. Fusion proteins includehomopolymers and heteropolymers, as described below.

In some embodiments, the peptide comprises or consists of multipleepitopes and/or analogs, e.g., 2, 3, 4, 5, 6, 7, 8, 9 or 10 epitopesand/or analogs of the invention. In some embodiments, the peptidecomprises at least 1, at least 2, at least 3, at least 4, at least 5, atleast 6, at least 7, at least 8, at least 9 or at least 10 epitopesand/or analogs of the invention.

The peptide may also exclude any one or several epitopes and/or analogsselected from those in Table 3 (SEQ ID NOs:1-10). Epitopes/analogs whichmay preferably be excluded from peptides of the invention are SEQ IDNOs:1-10.

The peptide may also be a homopolymer of one epitope or analog or thepeptide may be a heteropolymer which contains at least two differentepitopes and/or analogs. Polymers have the advantage of increasedprobability for immunological reaction and, where differentepitopes/analogs are used to make up the polymer, the ability to induceantibodies and/or T cells that react with different antigenicdeterminants of the antigen(s) targeted for an immune response.

A homopolymer may comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 copies ofthe same epitope or analog.

A heteropolymer may comprise one or more copies of an individual epitopeor analog and one or more copies of one or more different epitopesand/or analogs of the invention. The epitopes and/or analogs that form aheteropolymer may all be from the same antigen, e.g., may be from CEA,p53, MAGE2/3, HER2/neu or other antigens herein or known in the art, ormay be from different antigens, preferably TAAs. Combinations ofepitopes and/or analogs that may form a heteropolymer include thosecombinations described above. Heteropolymers may contain multiple copiesof one or more epitopes and/or analogs.

Thus, peptides of the invention such as heteropolymers may comprise afirst epitope and/or analog and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,47, 48, 49, or 50 other (different) epitopes and/or analogs.

Peptides of the invention may also comprise additional amino acidresidues.

In some embodiments, the peptides may also comprise a number of CTLand/or HTL epitopes, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 CTL and/or HTL epitopes.

The CTL and/or HTL epitope and the epitope/analog of the invention maybe from the same TAA or from different TAAs. Thus, for example, if theepitope and/or analog is from CEA, the CTL peptide and/or HTL peptidemay also be from CEA. Alternatively, the CTL peptide and/or HTL peptidemay be from another antigen, preferably a TAA antigen such as p53,MAGE2/3 or HER2/neu. As another example, if the epitope and/or analog isfrom p53, the CTL peptide and/or HTL peptide may be from p53 or,alternatively, may be from MAGE2/3, HER2/neu, or CEA.

The CTL peptide and/or HTL peptide may be from tumor-associated antigenssuch as but not limited to, melanoma antigens MAGE-1, MAGE-2, MAGE-3,MAGE-11, MAGE-A10, as well as BAGE, GAGE, RAGE, MAGE-C1, LAGE-1, CAG-3,DAM, MUC1, MUC2, MUC18, NY-ESO-1, MUM-1, CDK4, BRCA2, NY-LU-1, NY-LU-7,NY-LU-12, CASP8, RAS, KTAA-2-5, SCCs, p53, p73, CEA, HER1/neu, Melan-A,gp100, tyrosinase, TRP2, gp75/TRP1, kallikrein, prostate-specificmembrane antigen (PSM), prostatic acid phosphatase (PAP),prostate-specific antigen (PSA), PT1-1, β-catenin, PRAME, Telomerase,FAK, cyclin D1 protein, NOEY2, EGF-R, SART-1, CAPB, HPVE7, p15, Folatereceptor CDC27, PAGE-1, and PAGE-4 (See, e.g., Table 16).

Non-limiting examples of CTL peptides and HTL peptides are disclosed inWO 01/42270, published 14 Jun. 2001; WO 01/41788, published 14 Jun.2001; WO 01/42270, published 14 Jun. 2001; WO 01/45728, published 28Jun. 2001; and WO 01/41787, published 14 Jun. 2001.

The HTL peptide may comprise a synthetic peptide such as aPan-DR-binding epitope (e.g., a PADRE® peptide, Epimmune Inc., SanDiego, Calif., described, for example, in U.S. Pat. No. 5,736,142), forexample, having the formula aKXVAAZTLKAAa, where “X” is eithercyclohexylalanine, phenylalanine, or tyrosine; “Z” is either tryptophan,tyrosine, histidine or asparagine; and “a” is either D-alanine orL-alanine (SEQ ID NO: 746). Certain pan-DR binding epitopes comprise all“L” natural amino acid residues; these molecules can be provided aspeptides or in the form of nucleic acids that encode the peptide. Seealso, U.S. Pat. Nos. 5,679,640 and 6,413,935.

The peptide may comprise additional amino acid residues. Such additionalamino acid residues may be Ala, Arg, Asn, Asp, Cys, Gln, Gly, Glu, H is,Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Tyr, Trp, Val, amino acidmimetics, and other unnatural amino acid residues such as thosedescribed below. Additional amino acid residues may provide for ease oflinking peptides one to another, for linking epitopes and/or analogs toone another, for linking epitopes and/or analogs to CTL and/or HTLepitopes, for coupling to a carrier support or larger peptide, formodifying the physical or chemical properties of the peptide, oroligopeptide, or the like. Amino acid residues such as Ala, Arg, Asn,Asp, Cys, Gln, Gly, Glu, H is, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr,Tyr, Trp, or Val, or the like, can be introduced at the C- and/orN-terminus of the peptide and/or can be introduced internally.

The peptide may comprise an amino acid spacer, which may be joined tothe epitopes, analogs, CTL epitopes, HTL epitopes, carriers, etc. withina peptide or may be joined to the peptide at the N-and/or C-terminus.Thus, spacers may be at the N-terminus or C-terminus of peptide, or maybe internal such that they link or join epitopes, analogs, CTL epitopes,HTL epitopes, carriers, additional amino acid residues, and/or antigenicfragments one to the other.

The spacer is typically comprised of one or more relatively small,neutral molecules, such as amino acid residues or amino acid mimetics,which are substantially uncharged under physiological conditions. Thespacers are typically selected from, e.g., Ala, Gly, or other neutralspacers of nonpolar amino acid residues or neutral polar amino acidresidues. It will be understood that the optionally present spacer maybe composed of the same residues or may be composed of one or moredifferent residues and thus may be a homo- or hetero-oligomer of spacerresidues. Thus, the spacer may contain more than one Ala residue(poly-alanine) or more than one Gly residue (poly-glycine), or maycontain both Ala and Gly residues, e.g., Gly, Gly-Gly-, Ser,Ser-Ser-,Gly-Ser-, Ser-Gly-, etc. When present, the spacer will usually be atleast one or two residues, more usually three to six residues andsometimes 10 or more residues, e.g., 3, 4, 5, 6, 7, 8, 9, or 10, or evenmore residues. (Livingston, B. D. et al. Vaccine 19:46524660 (2000)).

Peptides may comprise carriers such as those well known in the art,e.g., thyroglobulin, albumins such as human serum albumin, tetanustoxoid, polyamino acid residues such as poly L-lysine, poly L-glutamicacid, influenza virus proteins, hepatitis B virus core protein, and thelike.

In addition, the peptide may be modified by terminal-NH₂ acylation,e.g., by alkanoyl (C₁-C₂₀) or thioglycolyl acetylation,terminal-carboxyl amidation, e.g., ammonia, methylamine, etc. In someinstances these modifications may provide sites for linking to a supportor other molecule.

The peptides in accordance with the invention can contain modificationssuch as but not limited to glycosylation, side chain oxidation,biotinylation, phosphorylation, addition of a surface active material,e.g. a lipid, or can be chemically modified, e.g., acetylation, etc.Moreover, bonds in the peptide can be other than peptide bonds, e.g.,covalent bonds, ester or ether bonds, disulfide bonds, hydrogen bonds,ionic bonds, etc.

Peptides of the present invention may contain substitutions to modify aphysical property (e.g., stability or solubility) of the resultingpeptide. For example, peptides may be modified by the substitution of acysteine (C) with α-amino butyric acid (“B”). Due to its chemicalnature, cysteine has the propensity to form disulfide bridges andsufficiently alter the peptide structurally so as to reduce bindingcapacity. Substituting α-amino butyric acid for C not only alleviatesthis problem, but actually improves binding and crossbinding capabilityin certain instances. Substitution of cysteine with α-amino butyric acidmay occur at any residue of a peptide, e.g., at either anchor ornon-anchor positions of an epitope or analog within a peptide, or atother positions of a peptide.

The peptides can comprise amino acid mimetics or unnatural, amino acidresidues, e.g. D- or L-naphylalanine; D- or L-phenylglycine; D- orL-2-thieneylalanine; D- or L-1, -2,3-, or 4-pyreneylalanine; D- or L-3thieneylalanine; D- or L-(2-pyridinyl)-alanine; D- orL-(3-pyridinyl)-alanine; D- or L-(2-pyrazinyl)-alanine; D- orL-(4-isopropyl)-phenylglycine; D-(trifluoromethyl)-phenylglycine;D-(trifluoro-methyl)-phenylalanine; D-p-fluorophenylalanine; D- orL-p-biphenyl-phenylalanine; D- or L-ρ-methoxybiphenylphenylalanine; D-or L-2-indole(alkyl)alanines; and, D- or L-alkylalanines, where thealkyl group can be a substituted or unsubstituted methyl, ethyl, propyl,hexyl, butyl, pentyl, isopropyl, iso-butyl, sec-isotyl, iso-pentyl, or anon-acidic amino acid residues. Aromatic rings of a non-natural aminoacid include, e.g., thiazolyl, thiophenyl, pyrazolyl, benzimidazolyl,naphthyl, furanyl, pyrrolyl, and pyridyl aromatic rings. Modifiedpeptides that have various amino acid mimetics or unnatural amino acidresidues are particularly useful, as they tend to manifest increasedstability in vivo. Such peptides may also possess improved shelf-life ormanufacturing properties.

Peptide stability can be assayed in a number of ways. For instance,peptidases and various biological media, such as human plasma and serum,have been used to test stability. See, e.g., Verhoef, et al., Eur. J.Drug Metab. Pharmacokinetics 11:291 (1986). Half-life of the peptides ofthe present invention is conveniently determined using a 25% human serum(v/v) assay. The protocol is generally as follows: Pooled human serum(Type AB, non-heat inactivated) is delipidated by centrifugation beforeuse. The serum is then diluted to 25% with RPMI-1640 or another suitabletissue culture medium. At predetermined time intervals, a small amountof reaction solution is removed and added to either 6% aqueoustrichloroacetic acid (TCA) or ethanol. The cloudy reaction sample iscooled (4° C.) for 15 minutes and then spun to pellet the precipitatedserum proteins. The presence of the peptides is then determined byreversed-phase HPLC using stability-specific chromatography conditions.

The peptides in accordance with the invention can be a variety oflengths, and either in their neutral (uncharged) forms or in forms whichare salts. The peptides in accordance with the invention can containmodifications such as glycosylation, side chain oxidation, orphosphorylation, generally subject to the condition that modificationsdo not destroy the biological activity of the peptides.

The peptides of the invention may be lyophylized, or may be in crystalform.

It is generally preferable that the epitope be as small as possiblewhile still maintaining substantially all of the immunologic activity ofthe native protein. When possible, it may be desirable to optimize HLAclass I binding epitopes of the invention to a length of about 8 toabout 13 amino acid residues, for example, 8, 9, 10, 11, 12 or 13,preferably 9 or 10. It is to be appreciated that one or more epitopes inthis size range can be comprised by a longer peptide (see the DefinitionSection for the term “epitope” for further discussion of peptidelength). HLA class II binding epitopes are preferably optimized to alength of about 6 to about 30 amino acid residues in length, e.g., 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29 or 30, preferably to between about 13 and about 20residues, e.g., 13, 14, 15, 16, 17, 18, 19 or 20. Preferably, theepitopes are commensurate in size with endogenously processedpathogen-derived peptides or tumor cell peptides that are bound to therelevant HLA molecules. The identification and preparation of peptidesof various lengths can be carried out using the techniques describedherein.

Peptides in accordance with the invention can be prepared synthetically,by recombinant DNA technology or chemical synthesis, or can be isolatedfrom natural sources such as native tumors or pathogenic organisms.Epitopes may be synthesized individually or joined directly orindirectly in a peptide. Although the peptide will preferably besubstantially free of other naturally occurring host cell proteins andfragments thereof, in some embodiments the peptides may be syntheticallyconjugated to be joined to native fragments or particles.

The peptides of the invention can be prepared in a wide variety of ways.For relatively short sizes, the peptides can be synthesized in solutionor on a solid support in accordance with conventional techniques.Various automatic synthesizers are commercially available and can beused in accordance with known protocols. (See, for example, Stewart &Young, SOLID PHASE PEPTIDE SYNTHESIS, 2D. ED., Pierce Chemical Co.,1984). Further, individual peptides can be joined using chemicalligation to produce larger peptides that are still within the bounds ofthe invention.

Alternatively, recombinant DNA technology can be employed wherein anucleotide sequence which encodes a peptide inserted into an expressionvector, transformed or transfected into an appropriate host cell andcultivated under conditions suitable for expression. These proceduresare generally known in the art, as described generally in Sambrook etal., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Press,Cold Spring Harbor, N.Y. (1989). Thus, recombinant peptides, whichcomprise or consist of one or more epitopes of the invention, can beused to present the appropriate T cell epitope.

Polynucleotides encoding each of the peptides above are also part of theinvention. As appreciated by one of ordinary skill in the art, variousnucleic acids will encode the same peptide due to the redundancy of thegenetic code. Each of these nucleic acids falls within the scope of thepresent invention. This embodiment of the invention comprises DNA andRNA, and in certain embodiments a combination of DNA and RNA. It is tobe appreciated that any polynucleotide that encodes a peptide inaccordance with the invention falls within the scope of this invention.

The polynucleotides encoding peptides contemplated herein can besynthesized by chemical techniques, for example, the phosphotriestermethod of Matteucci, et al., J. Am. Chem. Soc. 103:3185 (1981).Polynucleotides encoding peptides comprising or consisting of an analogcan be made simply by substituting the appropriate and desired nucleicacid base(s) for those that encode the native epitope.

The polynucleotide, e.g. minigene (see below), may be produced byassembling oligonucleotides that encode the plus and minus strands ofthe polynucleotide, e.g. minigene. Overlapping oligonucleotides (15-100bases long) may be synthesized, phosphorylated, purified and annealedunder appropriate conditions using well known techniques. The ends ofthe oligonucleotides can be joined, for example, using T4 DNA ligase. Apolynucleotide, e.g. minigene, encoding the peptide of the invention,can be cloned into a desired vector such as an expression vector. Thecoding sequence can then be provided with appropriate linkers andligated into expression vectors commonly available in the art, and thevectors used to transform suitable hosts to produce the desired peptidesuch as a fusion protein.

A large number of such vectors and suitable host systems are known tothose of skill in the art, and are commercially available. The followingvectors are provided by way of example. Bacterial: pQE70, pQE60, pQE-9(Qiagen), pBS, pD10, phagescript, psiX174, pBluescript SK, pbsks, pNH₈A,pNH16a, pNH18A, pNH46A (Stratagene); ptrc99a, pKK223-3, pKK233-3,pDR540, pRIT5 (Pharmacia); pCR (Invitrogen). Eukaryotic: pWLNEO,pSV2CAT, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL(Pharmacia); p75.6 (Valentis); pCEP (Invitrogen); pCEI (Epimmune).However, any other plasmid or vector can be used as long as it isreplicable and viable in the host.

As representative examples of appropriate hosts, there can be mentioned:bacterial cells, such as E. coli, Bacillus subtilis, Salmonellatyphimurium and various species within the genera Pseudomonas,Streptomyces, and Staphylococcus; fungal cells, such as yeast; insectcells such as Drosophila and Sf9; animal cells such as COS-7 lines ofmonkey kidney fibroblasts, described by Gluzman, Cell 23:175 (1981), andother cell lines capable of expressing a compatible vector, for example,the C127, 3T3, CHO, HeLa and BHK cell lines or Bowes melanoma; plantcells, etc. The selection of an appropriate host is deemed to be withinthe scope of those skilled in the art from the teachings herein.

Thus, the present invention is also directed to vectors, preferablyexpression vectors useful for the production of the peptides of thepresent invention, and to host cells comprising such vectors.

Host cells are genetically engineered (transduced or transformed ortransfected) with the vectors of this invention which can be, forexample, a cloning vector or an expression vector. The vector can be,for example, in the form of a plasmid, a viral particle, a phage, etc.The engineered host cells can be cultured in conventional nutrient mediamodified as appropriate for activating promoters, selectingtransformants or amplifying the polynucletides. The culture conditions,such as temperature, pH and the like, are those previously used with thehost cell selected for expression, and will be apparent to theordinarily skilled artisan.

For expression of the peptides, the coding sequence will be providedwith operably linked start and stop codons, promoter and terminatorregions and usually a replication system to provide an expression vectorfor expression in the desired cellular host. For example, promotersequences compatible with bacterial hosts are provided in plasmidscontaining convenient restriction sites for insertion of the desiredcoding sequence. The resulting expression vectors are transformed intosuitable bacterial hosts.

Generally, recombinant expression vectors will include origins ofreplication and selectable markers permitting transformation of the hostcell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiaeTRP1 gene, and a promoter derived from a highly-expressed gene to directtranscription of a downstream structural sequence. Such promoters can bederived from operons encoding glycolytic enzymes such as3-phosphoglycerate kinase (PGK), ∀-factor, acid phosphatase, or heatshock proteins, among others. The heterologous structural sequence isassembled in appropriate phase with translation initiation andtermination sequences, and preferably, a leader sequence capable ofdirecting secretion of translated protein into the periplasmic space orextracellular medium. Optionally, the heterologous sequence can encode afusion protein including an N-terminal identification peptide impartingdesired characteristics, e.g., stabilization or simplified purificationof expressed recombinant product.

Yeast, insect or mammalian cell hosts may also be used, employingsuitable vectors and control sequences. Examples of mammalian expressionsystems include the COS-7 lines of monkey kidney fibroblasts, describedby Gluzman, Cell 23:175 (1981), and other cell lines capable ofexpressing a compatible vector, for example, the C127, 3T3, CHO, HeLaand BHK cell lines. Mammalian expression vectors will comprise an originof replication, a suitable promoter and enhancer, and also any necessaryribosome binding sites, polyadenylation site, splice donor and acceptorsites, transcriptional termination sequences, and 5″ flankingnontranscribed sequences. Such promoters may also be derived from viralsources, such as, e.g., human cytomegalovirus (CMV-IE promoter) orherpes simplex virus type-1 (HSV TK promoter). Nucleic acid sequencesderived from the SV40 splice, and polyadenylation sites can be used toprovide the required nontranscribed genetic elements.

Polynucleotides encoding peptides of the invention may also comprise aubiquitination signal sequence, and/or a targeting sequence such as anendoplasmic reticulum (ER) signal sequence to facilitate movement of theresulting peptide into the endoplasmic reticulum.

Polynucleotides of the invention, e.g., minigenes, may be expressed inhuman cells. A human codon usage table can be used to guide the codonchoice for each amino acid. Such polynucleotides preferably comprisespacer amino acid residues between epitopes and/or analogs, such asthose described above, or may comprise naturally-occurring flankingsequences adjacent to the epitopes and/or analogs (and/or CTL and HTLepitopes).

The peptides of the invention can also be expressed by viral orbacterial vectors. Examples of expression vectors include attenuatedviral hosts, such as vaccinia or fowlpox. As an example of thisapproach, vaccinia virus is used as a vector to express nucleotidesequences that encode the peptides of the invention. Vaccinia vectorsand methods useful in immunization protocols are described in, e.g.,U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille CalmetteGuerin). BCG vectors are described by Stover et al., Nature 351:456-460(1991). A wide variety of other vectors useful for therapeuticadministration or immunization of the polypeptides of the invention,e.g. adeno and adeno-associated virus vectors, retroviral vectors,Salmonella typhi vectors, detoxified anthrax toxin vectors, and thelike, will be apparent to those skilled in the art from the descriptionherein. A preferred vector is Modified Vaccinia Ankara (MVA) (e.g.,Bavarian Noridic (MVA-BN)).

Standard regulatory sequences well known to those of skill in the artare preferably included in the vector to ensure expression in the humantarget cells. Several vector elements are desirable: a promoter with adownstream cloning site for polynucleotide, e.g., minigene insertion; apolyadenylation signal for efficient transcription termination; an E.coli origin of replication; and an E. colt selectable marker (e.g.ampicillin or kanamycin resistance). Numerous promoters can be used forthis purpose, e.g., the human cytomegalovirus (hCMV) promoter. See,e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promotersequences. A preferred promoter is the CMV-IE promoter.

Polynucleotides, e.g. minigenes, may comprise one or more synthetic ornaturally-occurring introns in the transcribed region. The inclusion ofmRNA stabilization sequences and sequences for replication in mammaliancells may also be considered for increasing polynucleotide, e.g.minigene, expression.

In addition, the polynucleotide, e.g. minigene, may compriseimmunostimulatory sequences (ISSs or CpGs). These sequences may beincluded in the vector, outside the polynucleotide (e.g. minigene)coding sequence to enhance immunogenicity.

In some embodiments, a bi-cistronic expression vector which allowsproduction of both the polynucleotide (e.g. minigene) encoded peptidesof the invention and a second protein (e.g., one that modulatesimmunogenicity) can be used. Examples of proteins or polypeptides that,if co-expressed with peptides of the invention, can enhance an immuneresponse include cytokines (e.g., IL-2, IL-12, GM-CSF),cytokine-inducing molecules (e.g., Lea), costimulatory molecules, orpan-DR binding proteins (PADRE® molecules, Epimmune, San Diego, Calif.).Helper T cell (HTL) epitopes such as PADRE® molecules can be joined tointracellular targeting signals and expressed separately from expressedpeptides of the invention. Specifically decreasing the immune responseby co-expression of immunosuppressive molecules (e.g. TGF-β) may bebeneficial in certain diseases.

Once an expression vector is selected, the polynucleotide, e.g.minigene, is cloned into the polylinker region downstream of thepromoter. This plasmid is transformed into an appropriate bacterialstrain, and DNA is prepared using standard techniques. The orientationand DNA sequence of the polynucleotide, e.g. minigene, as well as allother elements included in the vector, are confirmed using restrictionmapping, DNA sequence analysis, and/or PCR analysis. Bacterial cellsharboring the correct plasmid can be stored as cell banks.

Therapeutic/prophylactic quantities of DNA can be produced for example,by fermentation in E. coli, followed by purification. Aliquots from theworking cell bank are used to inoculate growth medium, and are grown tosaturation in shaker flasks or a bioreactor according to well knowntechniques. Plasmid DNA is purified using standard bioseparationtechnologies such as solid phase anion-exchange resins available, e.g.,from QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA canbe isolated from the open circular and linear forms using gelelectrophoresis or other methods.

Purified polynucleotides, e.g. minigenes, can be prepared for injectionusing a variety of formulations. The simplest of these is reconstitutionof lyophilized polynucleotide, e.g. DNA, in sterile phosphate-buffersaline (PBS). This approach, known as “naked DNA,” is currently beingused by others for intramuscular (IM) administration in clinical trials.To maximize the immunotherapeutic effects of polynucleotide vaccines,alternative methods of formulating purified plasmid DNA may be used. Avariety of such methods have been described, and new techniques maybecome available. Cationic lipids, glycolipids, and fusogenic liposomescan also be used in the formulation (see, e.g., WO 93/24640; Mannino &Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833;WO 91/06309; and Feigner, et al., Proc. Nat'l Acad. Sci. USA 84:7413(1987). In addition, peptides and compounds referred to collectively asprotective, interactive, non-condensing compounds (PINC) can also becomplexed to purified plasmid DNA to influence variables such asstability, intramuscular dispersion, or trafficking to specific organsor cell types.

Known methods in the art can be used to enhance delivery and uptake of apolynucleotide in vivo. For example, the polynucleotide can be complexedto polyvinylpyrrolidone (PVP), to prolong the localized bioavailabilityof the polynucleotide, thereby enhancing uptake of the polynucleotide bythe organisum (see e.g., U.S. Pat. No. 6,040,295; EP 0 465 529; WO98/17814). This approache is thought to be more effective thaninoculation with merely “naked” DNA. PVP is a polyamide that is known toform complexes with a wide variety of substances, and is chemically andphysiologically inert.

Target cell sensitization can be used as a functional assay of theexpression and HLA class I presentation of polynucleotide- (e.g.minigene-) encoded peptides. For example, the polynucleotide, e.g.plasmid DNA, is introduced into a mammalian cell line that is a suitabletarget for standard CTL chromium release assays. The transfection methodused will be dependent on the final formulation. For example,electroporation can be used for “naked” DNA, whereas cationic lipids orPVP-formulated DNA allow direct in vitro transfection. A plasmidexpressing green fluorescent protein (GFP) can be co-transfected toallow enrichment of transfected cells using fluorescence activated cellsorting (FACS). The transfected cells are then chromium-51 (⁵¹Cr)labeled and used as targets for epitope-specific CTLs. Cytolysis of thetarget cells, detected by ⁵¹Cr release, indicates both production andHLA presentation of, polynucleotide-, e.g. minigene-, encoded epitopesand/or analogs of the invention, or peptides comprising them. Expressionof HTL epitopes may be evaluated in an analogous manner using assays toassess HTL activity.

In vivo immunogenicity is a second approach for functional testing ofpolynucleotides, e.g. minigenes. Transgenic mice expressing appropriatehuman HLA proteins are immunized with the polynucleotide, e.g. DNA,product. The dose and route of administration are formulation dependent(e.g., IM for polynucleotide (e.g., naked DNA or PVP-formulated DNA) inPBS, intraperitoneal (IP) for lipid-complexed polynucleotide (e.g.,DNA)). Eleven to twenty-one days after immunization, splenocytes areharvested and restimulated for one week in the presence ofpolynucleotides encoding each peptide being tested. Thereafter, forpeptides comprising or consisting of epitopes and/or analogs, standardassays are conducted to determine if there is cytolysis ofpeptide-loaded, ⁵¹Cr-labeled target cells. Once again, lysis of targetcells that were exposed to epitopes and/or analogs corresponding tothose encoded by the polynucleotide, e.g. minigene, demonstratespolynucleotide, e.g., DNA, vaccine function and induction of CTLs.Immunogenicity of HTL epitopes is evaluated in transgenic mice in ananalogous manner.

Alternatively, the nucleic acids can be administered using ballisticdelivery as described, for instance, in U.S. Pat. No. 5,204,253. Usingthis technique, particles comprised solely of a polynucleotide such asDNA are administered. In a further alternative embodiment for ballisticdelivery, polynucleotides such as DNA can be adhered to particles, suchas gold particles.

The use of polynucleotides such as multi-epitope minigenes is describedherein and in, e.g. co-pending application U.S. Ser. No. 09/311,784;Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J.L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822,1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al.,Vaccine 16:426, 1998. For example, a polynucleotide such as amulti-epitope DNA plasmid can be engineered which encodes an epitopederived from multiple regions of a TAA (e.g., p53, HER2/neu, MAGE-2/3,or CEA), a pan-DR binding peptide such as the PADRE® universal helper Tcell epitope, and an endoplasmic reticulum-translocating signalsequence. As described in the sections above, a peptide/polynucleotidemay also comprise/encode epitopes that are derived from other TAAs.

Thus, the invention includes peptides as described herein,polynucleotides encoding each of said peptides, as well as compositionscomprising the peptides and polynucleotides, and includes methods forproducing and methods of using the peptides, polynucleotides, andcompositions, as further described below.

Compositions. In other embodiments, the invention is directed to acomposition comprising one or more peptides and/or a polynucleotide ofthe invention and optionally another component(s).

In some embodiments, the composition comprises or consists of multiplepeptides, e.g., 2, 3, 4, 5, 6, 7, 8, 9 or 10 peptides of the invention.In some embodiments, the composition comprises at least 2, at least 3,at least 4, at least 5, at least 6, at least 7, at least 8, at least 9or at least 10 peptides of the invention.

Compositions of the invention may comprise polynucleotides encoding theabove peptides and/or combinations of peptides.

The composition can comprise at least 2, at least 3, at least 4, atleast 5, at least 6, at least 7, at least 8, at least 9 or at least 10peptides and/or polynucleotides selected from those described above orbelow. At least one of the one or more peptides can be a heteropolymeror a homopolymer. Additionally, the composition can comprise a CTLand/or HTL epitope, which can be derived from a tumor-associatedantigen. The additional epitope can also be a PanDR binding molecule,(e.g., a PADRE® universal helper T cell epitope).

Optional components include excipients, diluents, proteins such aspeptides comprising a CTL epitope, and/or an HTL epitope such as apan-DR binding peptide (e.g., a PADRE® universal helper T cell epitope),and/or a carrier, polynucleotides encoding such proteins, lipids, orliposomes, as well as other components described herein. There arenumerous embodiments of compositions in accordance with the invention,such as a cocktail of one or more peptides and/or polynucleotides; oneor more peptides and/or analogs and one or more CTL and/or HTL epitopes;and/or nucleic acids that encode such peptides, e.g., minigenes.

Compositions may comprise one or more peptides (and/or polynucleotidessuch as minigenes) of the invention, along with one or more othercomponents as described above and herein. “One or more” refers to anywhole unit integer from 1-150, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65,70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140,145, or 150 peptides, polynucleotides, or other components.

Compositions of the invention may be, for example, polynucleotides or,polypeptides of the invention combined with or completed to cationiclipid formulations; lipopeptides (e.g., Vitiello, A. et al., J. Clin.Invest. 95:341, 1995), encapsulated e.g., inpoly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge,et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995); peptidecompositions contained in immune stimulating complexes (ISCOMS) (see,e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin ExpImmunol. 113:235-243, 1998); multiple antigen peptide systems (MAPS)(see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988;Tam, J.P., J. Immunol. Methods 196:17-32, 1996); viral, bacterial, or,fungal delivery vectors (Perkus, M. E. et al., In: Concepts in vaccinedevelopment, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. etal., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986;Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al.,J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535,1990); particles of viral or synthetic origin (e.g., Kofler, N. et al.,J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol.30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995);adjuvants (e.g., incomplete Freund's adjuvant) (Warren, H. S., Vogel, F.R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. etal., Vaccine 11:293, 1993); liposomes (Reddy, R. et al., J. Immunol.148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996); or,particle-absorbed cDNA or other polynucleotides of the invention (Ulmer,J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., andWebster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Conceptsin vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K.B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge,J. H. et al., Sem. Hematol. 30:16, 1993), etc. Toxin-targeted deliverytechnologies, also known as receptor mediated targeting, such as thoseof Avant Immunotherapeutics, Inc. (Needham, Mass.) or attached to astress protein, e.g., HSP 96 (Stressgen Biotechnologies Corp., Victoria,BC, Canada) can also be used.

Compositions of the invention comprise polynucleotide-mediatedmodalities. DNA or RNA encoding one or more of the peptides of theinvention can be administered to a patient. This approach is described,for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S.Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524;5,679,647; and, WO 98/04720. Examples of DNA-based delivery technologiesinclude “naked DNA” (see, e.g., U.S. Pat. No. 5,693,622), facilitatedDNA ((i.e., non-“naked DNA”) facilitated e.g., by combination withbupivicaine, polymers (e.g., PVP, PINC, etc.), peptide-mediated)delivery, cationic lipid complexes, and particle-mediated (“gene gun”)or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).Accordingly, peptides of the invention can be expressed by viral orbacterial vectors. Examples of expression vectors include attenuatedviral hosts, such as Modified Vaccinia Ankara (MVA) (e.g., BavarianNoridic), vaccinia or fowlpox. For example, vaccinia virus is used as avector to express nucleotide sequences that encode the peptides of theinvention. Upon introduction into an acutely or chronically infectedhost or into a non-infected host, the recombinant vaccinia virusexpresses the immunogenic peptide, and thereby elicits an immuneresponse. Vaccinia vectors and methods useful in immunization protocolsare described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG(Bacille Calmette Guerin). BCG vectors are described in Stover et al.,Nature 351:456-460 (1991). A wide variety of other vectors useful fortherapeutic administration or immunization of the peptides of theinvention, e.g. adeno and adeno-associated virus vectors, alpha virusvectors, retroviral vectors, Salmonella typhi vectors, detoxifiedanthrax toxin vectors, and the like, are apparent to those skilled inthe art from the description herein.

In certain embodiments, components that induce T cell responses arecombined with components that induce antibody responses to the targetantigen of interest. A preferred embodiment of such a compositioncomprises class I and class II epitopes in accordance with theinvention. Alternatively, a composition comprises a class I and/or classII epitope in accordance with the invention, along with a PADRE®molecule (Epimmune, San Diego, Calif.).

Compositions of the invention can comprise antigen presenting cells,such as dendritic cells. Antigen presenting cells, e.g., dendriticcells, may be transfected, e.g., with a polynucleotide such as aminigene construct in accordance with the invention, in order to elicitimmune responses. The peptide can be bound to an HLA molecule on theantigen-resenting cell, whereby when an HLA-restricted cytotoxic Tlymphocyte (CTL) is present, a receptor of the CTL binds to a complex ofthe HLA molecule and the peptide.

The compositions of the invention may also comprise antiviral drugs suchas interferon-α, or immune adjuvants such as IL-12, GM-CSF, etc.

Compositions may comprise an HLA heavy chain, β₂-microglobulin,streptavidin, and/or biotin. The streptavidin may be fluorescentlylabeled. Compositions may comprise tetramers (see e.g., U.S. Pat. No.5,635,363; Science 274:94-96 (1996)). A tetramer composition comprisingan HLA heavy chain, β₂-microglobulin, streptavidin, and biotin. Thestreptavidin may be fluorescently labeled. Compositions may alsocomprise dimers. A dimer composition comprises as MHC molecule and an Igmolecule (see e.g., Proc. Natl. Acad. Sci., USA, 95:7568-73 (1998)).

In some embodiments it may be desirable to include in the compositionsof the invention at least one component which primes cytotoxic Tlymphocytes. Lipids have been identified as agents capable of primingCTL in vivo against viral antigens. For example, palmitic acid residuescan be attached to the ε- and α-amino groups of a lysine residue andthen linked, e.g., via one or more linking residues such as Gly,Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. Thelipidated peptide can then be administered either directly in a micelleor particle, incorporated into a liposome, or emulsified in an adjuvant,e.g., incomplete Freund's adjuvant. A preferred composition comprisespalmitic acid attached to ε- and α-amino groups of Lys, which isattached via linkage, e.g., Ser-Ser, to the amino terminus of thepeptide.

As another example of lipid priming of CTL responses, E. colilipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine(P₃CSS) can be used to prime virus specific CTL when covalently attachedto an appropriate peptide (see, e.g., Deres, et al., Nature 342:561,1989). Peptides of the invention can be coupled to P₃CSS, for example,and the lipopeptide administered to an individual to specifically primea CTL response to the target antigen. Moreover, because the induction ofneutralizing antibodies can also be primed with P₃CSS-conjugatedepitopes, two such compositions can be combined to more effectivelyelicit both humoral and cell-mediated responses.

Another preferred embodiment is a composition comprising one or morepeptides of the invention emulsified in IFA.

A highly preferred embodiment of the invention comprises peptidescomprising SEQ ID NOs:1-10 of the invention emulsified in IFA.

Compositions of the invention may also comprise CTL and/or HTL peptides.Such CTL and HTL peptides can be modified by the addition of amino acidresidues to the termini of a peptide to provide for ease of linkingpeptides one to another, for coupling to a carrier support or largerpeptide, for modifying the physical or chemical properties of thepeptide or oligopeptide, or the like. Amino acid residues such astyrosine, cysteine, lysine, glutamic or aspartic acid, or naturally orunnaturally occurring amino acid residues, can be introduced at thecarboxyl- or amino-terminus of the peptide or oligopeptide, particularlyclass I peptides. However, it is to be noted that modification at thecarboxyl terminus of a CTL epitope may, in some cases, alter bindingcharacteristics of the peptide. In addition, the peptide or oligopeptidesequences can differ from the natural sequence by being modified byterminal-NH₂ acylation, e.g., by alkanoyl (C₁-C₂₀) or thioglycolylacetylation, terminal-carboxyl amidation, e.g., ammonia, methylamine,etc. In some instances these modifications may provide sites for linkingto a support or other molecule. CTL and HTL epitopes may compriseadditional amino acid residues, such as those described above includingspacers.

A further embodiment of a composition in accordance with the inventionis an antigen presenting cell that comprises one or more peptides inaccordance with the invention. The antigen presenting cell can be a“professional” antigen presenting cell, such as a dendritic cell. Theantigen presenting cell can comprise the peptide of the invention by anymeans known or to be determined in the art. Such means include pulsingof dendritic cells with one or more individual peptides, by nucleic acidadministration such as ballistic nucleic acid delivery or by othertechniques in the art for administration of nucleic acids, includingvector-based, e.g. viral vector, delivery of nucleic acids.

Compositions may comprise carriers. Carriers that can be used withcompositions of the invention are well known in the art, and include,e.g., thyroglobulin, albumins such as human serum albumin, tetanustoxoid, polyamino acid residues such as poly L-lysine, poly L-glutamicacid, influenza virus proteins, hepatitis B virus core protein, and thelike.

The compositions (e.g. pharmaceutical compositions) can contain aphysiologically tolerable diluent such as water, or a saline solution,preferably phosphate buffered saline. Additionally, as disclosed herein,CTL responses can be primed by conjugating peptides of the invention tolipids, such as tripalmitoyl-S-glyceryl-cysteinyl-seryl-serine (P₃CSS).

Compositions of the invention may be pharmaceutically acceptablecompositions. Pharmaceutical compositions preferably contain animmunologically effective amount of one or more peptides and/orpolynucleotides of the invention, and optionally one or more othercomponents which are pharmaceutically acceptable. A preferredcomposition comprises one or more peptides of the invention and IFA. Amore preferred composition of the invention comprises one or morepeptides of the invention, one or more peptides, and IFA.

Upon immunization with a peptide and/or polynucleotide and/orcomposition in accordance with the invention, via injection (e.g., SC,ID, IM), aerosol, oral, transdermal, transmucosal, intrapleural,intrathecal, or other suitable routes, the immune system of the hostresponds to the vaccine by an immune response comprising the productionof antibodies, CTLs and/or HTLs specific for the desired antigen(s).Consequently, the host becomes at least partially immune to subsequentexposure to the TAA(s), or at least partially resistant to furtherdevelopment of TAA-bearing cells and thereby derives a prophylactic ortherapeutic benefit.

Furthermore, the peptides, primers, and epitopes of the invention can beused in any desired immunization or administration regimen; e.g., aspart of periodic vaccinations such as annual vaccinations as in theveterinary arts or as in periodic vaccinations as in the human medicalarts, or as in a prime-boost regime wherein an inventive vector orrecombinant is administered either before or after the administration ofthe same or of a different epitope of interest or recombinant or vectorexpressing such as a same or different epitope of interest (including aninventive recombinant or vector expressing such as a same or differentepitope of interest), see, e.g., U.S. Pat. Nos. 5,997,878; 6,130,066;6,180,398; 6,267,965; and 6,348,450. An useful viral vector of thepresent invention is Modified Vaccinia Ankara (MVA) (e.g., BavarianNoridic (MVA-BN)).

Recent studies have indicated that a prime boost protocol, wherebyimmunization with a poxvirus recombinant expressing a foreign geneproduct is followed by a boost using a purified subunit preparation formof that gene product, elicits an enhanced immune response relative tothe response elicited with either product alone. Human volunteersimmunized with a vaccinia recombinant expressing the HIV-1 envelopeglycoprotein and boosted with purified HIV-1 envelope glycoproteinsubunit preparation exhibit higher HIV-1 neutralizing antibody titersthan individuals immunized with just the vaccinia recombinant orpurified envelope glycoprotein alone (Graham et al., J. Infect. Dis.,167:533-537 (1993); Cooney et al., Proc. Natl. Acad. Sci. USA,90:1882-1886 (1993)). Humans immunized with two injections of anALVAC-HIV-1 env recombinant (vCP125) failed to develop HIV specificantibodies. Boosting with purified rgp160 from a vaccinia virusrecombinant resulted in detectable HIV-1 neutralizing antibodies.Furthermore, specific lymphocyte T cell proliferation to rgp160 wasclearly increased by the boost with rgp160. Envelope specific cytotoxiclymphocyte activity was also detected with this vaccination regimen(Pialoux et al., AIDS Res. and Hum. Retroviruses, 11:272-381 (1995)).Macaques immunized with a vaccinia recombinant expressing the simianimmunodeficiency virus (SW) envelope glycoprotein and boosted with SWenvelope glycoprotein from a baculovirus recombinant are protectedagainst SW challenge (Hu et al., AID Res. and Hum. Retroviruses,3:615-620 (1991); Hu et al., Science 255:456-459 (1992)). In the samefashion, purified HCMVgB protein can be used in prime-boost protocolswith NYVAC or ALVAC-gB recombinants.

In certain embodiments, the polynucleotides are complexed in a liposomepreparation. Liposomal preparations for use in the instant inventioninclude cationic (positively charged), anionic (negatively charged) andneutral preparations. However, cationic liposomes are particularlypreferred because a tight charge complex can be formed between thecationic liposome and the polyanionic nucleic acid. Cationic liposomeshave been shown to mediate intracellular delivery of plasmid DNA(Feigner et al., Proc. Natl. Acad. Sci. USA 84:74137416 (1987), which isherein incorporated by reference); mRNA (Malone et al., Proc. Natl.Acad. Sci. USA 86:60776081 (1989), which is herein incorporated byreference); and purified transcription factors (Debs et al., J. Biol.Chem. 265:1018910192 (1990), which is herein incorporated by reference),in functional form.

Cationic liposomes are readily available. For example,N-[12,3-dioleyloxy)-propyl-N,N,N-triethylammonium (DOTMA) liposomes areparticularly useful and are available under the trademark Lipofectin®,from Invitrogen, Carlsbad, Calif. (See, also, Feigner et al., Proc.Natl. Acad. Sci. USA 84:74137416 (1987)). Other commercially availableliposomes include transfectace (DDAB/DOPE) and DOTAP/DOPE (Boehringer).

Other cationic liposomes can be prepared from readily availablematerials using techniques well known in the art. See, e.g. PCTPublication No. WO 90/11092 for a description of the synthesis of DOTAP(1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes. Preparationof DOTMA liposomes is explained in the literature, see, e.g., P. Feigneret al., Proc. Natl. Acad. Sci. USA 84:74137417. Similar methods can beused to prepare liposomes from other cationic lipid materials.

Similarly, anionic and neutral liposomes are readily available, such asfrom Avanti Polar Lipids (Birmingham, Ala.), or can be easily preparedusing readily available materials. Such materials include phosphatidyl,choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidylcholine (DOPC), dioleoylphosphatidyl glycerol (DOPG),dioleoylphoshatidyl ethanolamine (DOPE), among others. These materialscan also be mixed with the DOTMA and DOTAP starting materials inappropriate ratios. Methods for making liposomes using these materialsare well known in the art.

For example, commercially available dioleoylphosphatidyl choline (DOPC),dioleoylphosphatidyl glycerol (DOPG), and dioleoylphosphatidylethanolamine (DOPE) can be used in various combinations to makeconventional liposomes, with or without the addition of cholesterol.Thus, for example, DOPG/DOPC vesicles can be prepared by drying 50 mgeach of DOPG and DOPC under a stream of nitrogen gas into a sonicationvial. The sample is placed under a vacuum pump overnight and is hydratedthe following day with deionized water. The sample is then sonicated for2 hours in a capped vial, using a Heat Systems model 350 sonicatorequipped with an inverted cup (bath type) probe at the maximum settingwhile the bath is circulated at 15° C. Alternatively, negatively chargedvesicles can be prepared without sonication to produce multilamellarvesicles or by extrusion through nucleopore membranes to produceunilamellar vesicles of discrete size. Other methods are known andavailable to those of skill in the art.

The liposomes can comprise multilamellar vesicles (MLVs), smallunilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs), withSUVs being preferred. The various liposome nucleic acid complexes areprepared using methods well known in the art. See, e.g., Straubinger etal., Methods of Immunology 101:512527 (1983). For example, MLVscontaining nucleic acid can be prepared by depositing a thin film ofphospholipid on the walls of a glass tube and subsequently hydratingwith a solution of the material to be encapsulated. SUVs are prepared byextended sonication of MLVs to produce a homogeneous population ofunilamellar liposomes. The material to be entrapped is added to asuspension of preformed MLVs and then sonicated. When using liposomescontaining cationic lipids, the dried lipid film is resuspended in anappropriate solution such as sterile water or an isotonic buffersolution such as 10 mM Tris/NaCl, sonicated, and then the preformedliposomes are mixed directly with the DNA. The liposome and DNA form avery stable complex due to binding of the positively charged liposomesto the cationic DNA. SUVs find use with small nucleic acid fragments.LUVs are prepared by a number of methods, well known in the art.Commonly used methods include Ca²⁺-EDTA chelation (Papahadjopoulos etal., Biochim. Biophys. Acta 394:483 (1975); Wilson et al., Cell 17:77(1979)); ether injection (Deamer, D. and Bangham, A., Biochim. Biophys.Acta 443:629 (1976); Ostro et al., Biochem. Biophys. Res. Commun. 76:836(1977); Fraley et al., Proc. Natl. Acad. Sci. USA 76:3348 (1979));detergent dialysis (Enoch, H. and Strittmatter, P., Proc. Natl. Acad.Sci. USA 76:145 (1979)); and reversephase evaporation (REV) (Fraley etal., J. Biol. Chem. 255:10431 (1980); Szoka, F. and Papahadjopoulos, D.,Proc: Natl. Acad. Sci. USA 75:145 (1978); SchaeferRidder et al., Science215:166 (1982)).

Generally, the ratio of DNA to liposomes will be from about 10:1 toabout 1:10. Preferably, the ration will be from about 5:1 to about 1:5.More preferably, the ration will be about 3:1 to about 1:3. Still morepreferably, the ratio will be about 1:1.

U.S. Pat. No. 5,676,954 reports on the injection of genetic material,complexed with cationic liposome carriers, into mice. U.S. Pat. Nos.4,897,355, 4,946,787, 5,049,386, 5,459,127, 5,589,466; 5,693,622,5,580,859, 5,703,055, and international publication no., WO 94/9469provide cationic lipids for use in transfecting DNA into cells andmammals. U.S. Pat. Nos. 5,589,466, 5,693,622, 5,580,859, 5,703,055, andinternational publication no. WO 94/9469 provide methods for deliveringDNA-cationic lipid complexes to mammals.

Binding Affinity of Epitopes and Analogs for HLA Molecules

As indicated herein, the large degree of HLA polymorphism is animportant factor to be taken into account with the epitope-basedapproach to developing therapeutics and diagnostics. To address thisfactor, epitope selection encompassing identification of peptidescapable of binding at high or intermediate affinity to multiple HLAmolecules is preferably utilized, most preferably these epitopes bind athigh or intermediate affinity to two or more allele-specific HLAmolecules. However, in some embodiments, it is preferred that allepitopes in a given composition bind to the alleles of a single HLAsupertype or a single HLA molecule.

Epitopes and analogs of the invention preferably include those that havean IC₅₀ or binding affinity value for a class I HLA molecule(s) of 500nM or better (i.e., the value is ≦500 nM). In certain embodiments of theinvention, peptides of interest have an IC₅₀ or binding affinity valuefor a class I HLA molecule(s) of 200 nM or better. In certainembodiments of the invention, peptides of interest, have an IC₅₀ orbinding affinity value for a class I HLA molecule(s) of 100 nM orbetter. If HTL epitopes are included, they preferably are HTL epitopesthat have an IC₅₀ or binding affinity value for class II HLA moleculesof 1000 nM or better, (i.e., the value is 5 1,000 nM). For example,peptide binding is assessed by testing the capacity of a candidatepeptide to bind to a purified HLA molecule in vitro. Peptides exhibitinghigh or intermediate affinity are then considered for further analysis.Selected peptides are generally tested on other members of the supertypefamily. In preferred embodiments, peptides that exhibit cross-reactivebinding are then used in cellular screening analyses or vaccines.

The relationship between binding affinity for HLA class I molecules andimmunogenicity of discrete peptide epitopes on bound antigens wasdetermined for the first time by inventors at Epimmune. As disclosed ingreater detail herein, higher HLA binding affinity is correlated withgreater immunogenicity.

Greater immunogenicity can be manifested in several different ways.Immunogenicity corresponds to whether an immune response is elicited atall, and to the vigor of any particular response, as well as to theextent of a population in which a response is elicited. For example, apeptide might elicit an immune response in a diverse array of thepopulation, yet in no instance produce a vigorous response. Inaccordance with these principles, close to 90% of high binding peptideshave been found to elicit a response and thus be “immunogenic,” ascontrasted with about 50% of the peptides that bind with intermediateaffinity. (See, e.g., Schaeffer et al. Proc. Natl. Acad. Sci., USA(1988)) High affinity-binding class I peptides generally have anaffinity of less than or equal to 100 nM. Moreover, not only didpeptides with higher binding affinity have an enhanced probability ofgenerating an immune response, the generated response tended to be morevigorous than the response seen with weaker binding peptides. As aresult, less peptide is required to elicit a similar biological effectif a high affinity binding peptide is used rather than a lower affinityone. Thus, in some preferred embodiments of the invention, high affinitybinding epitopes are used.

The correlation between binding affinity and immunogenicity was analyzedby the present inventors by two different experimental approaches (see,e.g., Sette, et al., J. Immunol. 153:5586-5592 (1994)). In the firstapproach, the immunogenicity of potential epitopes ranging in HLAbinding affinity over a 10,000-fold range was analyzed in HLA-A*0201transgenic mice. In the second approach, the antigenicity ofapproximately 100 different hepatitis B virus (HBV)-derived potentialepitopes, all carrying A*0201 binding motifs, was assessed by using PBLfrom acute hepatitis patients. Pursuant to these approaches, it wasdetermined that an affinity threshold value of approximately 500 nM(preferably 50 nM or less) determines the capacity of a peptide epitopeto elicit a CTL response. These data are true for class I bindingaffinity measurements for naturally processed peptides and forsynthesized T cell epitopes. These data also indicate the important roleof determinant selection in the shaping of T cell responses (see, e.g.,Schaeffer et al. Proc. Natl. Acad. Sci. USA 86:4649-4653 (1989)).

An affinity threshold associated with immunogenicity in the context ofHLA class II (i.e., HLA DR) molecules has also been delineated (see,e.g., Southwood et al. J. Immunology 160:3363-3373 (1998), and U.S. Pat.No. 6,413,527, issued Jul. 2, 2002). In order to define a biologicallysignificant threshold of HLA class II binding affinity, a database ofthe binding affinities of 32 DR-restricted epitopes for theirrestricting element (i.e., the HLA molecule that binds the epitope) wascompiled. In approximately half of the cases (15 of 32 epitopes), DRrestriction was associated with high binding affinities, i.e. bindingaffinity values of 100 nM or less. In the other half of the cases (16 of32), DR restriction was associated with intermediate affinity (bindingaffinity values in the 100-1000 nM range). In only one of 32 cases wasDR restriction associated with an IC₅₀ of 1000 nM or greater. Thus, 1000nM is defined as an affinity threshold associated with immunogenicity inthe context of DR molecules.

Epitope Binding Motifs and Supermotifs

Through the study of single amino acid substituted antigen analogs andthe sequencing of endogenously bound, naturally processed peptides,critical residues required for allele-specific binding to HLA moleculeshave been identified. The presence of these residues in a peptidecorrelates with both the probability of binding and with bindingaffinity for HLA molecules.

The identification of motifs and/or supermotifs that correlate with highand intermediate affinity binding is important when identifyingimmunogenic peptide epitopes for the inclusion in a vaccine. Kast et al.(J. Immunol. 152:3904-3912 (1994)) have shown that motif-bearingpeptides account for 90% of the epitopes that bind to allele-specificHLA class I molecules. In the Kast study, all possible 9 amino acid longpeptides, each overlapping by eight amino acid residues, which cover theentire sequence of the E6 and E7 proteins of human papillomavirus type16 were generated, which produced 240 peptides. All 240 peptides wereevaluated for binding to five allele-specific HLA molecules that areexpressed at high frequency among different ethnic groups. This unbiasedset of peptides allowed an evaluation of the predictive values of HLAclass I motifs. From the set of 240 peptides, 22 peptides wereidentified that bound to an allele-specific HLA molecule with high orintermediate affinity. Of these 22 peptides, 20 (i.e. 91%) weremotif-bearing. Thus, this study demonstrated the value of motifs foridentification of peptide epitopes to be included in a vaccine.

Accordingly, the use of motif-based identification techniques identifiesapproximately 90% of all potential epitopes in a target proteinsequence. Without the disclosed motif analysis, the ability topractically identify immunogenic peptide(s) for use in diagnostics ortherapeutics is seriously impaired.

Peptides, pharmaceutical compositions and vaccines of the presentinvention may also comprise epitopes that bind to MHC class II DRmolecules. A greater degree of heterogeneity in both size and bindingframe position of the motif, relative to the N- and C-termini of thepeptide, exists for class II peptide ligands. This increasedheterogeneity of HLA class II peptide ligands is due to the structure ofthe binding groove of the HLA class II molecule which, unlike its classI counterpart, is less physically constricted at both ends.Crystallographic analysis of HLA class II DRB*0101-peptide complexes toidentify the residues associated with major binding energy identifiedthose residues complexed with complementary pockets on the DRBI*0101molecules. An important anchor residue engages the deepest hydrophobicpocket (see, e.g., Madden, D. R. Ann. Rev. Immunol. 13:587 (1995)) andis referred to as position 1 (P1). P1 may represent the N-terminalresidue of a class II binding peptide epitope, but more typically isflanked towards the N-terminus by one or more residues. Other studieshave also pointed to an important role for the peptide residue in thesixth position towards the C-terminus, relative to P1, for binding tovarious DR molecules. See, e.g., U.S. Pat. No. 5,736,142, and co-pendingapplications entitled Alteration Of Immune Responses Using Pan DRBinding Peptides, U.S. Ser. No. 09/709,774, filed Nov. 8, 2000 and09/707,738, filed Nov. 6, 2000.

HLA-A2 Supermotif

Primary anchor specificities for allele-specific HLA-A2.1 molecules(see, e.g., Falk et al., Nature 351:290-296 (1991); Hunt et al., Science255:1261-1263 (1992); Parker et al., J. Immunol. 149:3580-3587 (1992);Ruppert et al., Cell 74:929-937 (1993)) and cross-reactive binding amongHLA-A2 and -A28 molecules have been described. (See, e.g., Fruci et al.,Human Immunol. 38:187-192 (1993); Tanigaki et al., Human Immunol.39:155-162 (1994); del Guercio et al., J. Immunol. 154:685-693 (1995);Kast et al., J. Immunol. 152:3904-3912 (1994) for reviews of relevantdata.) These primary anchor residues define the HLA-A2 supermotif; whichwhen present in peptide ligands corresponds to the ability to bindseveral different HLA-A2 and -A28 molecules. The HLA-A2 supermotifcomprises peptide ligands with L, I, V, M, A, T, or Q as a primaryanchor residue at position 2 and L, I, V, M, A, or T as a primary anchorresidue at the C-terminal position of the epitope.

The corresponding family of HLA molecules (i.e., the HLA-A2 supertypethat binds these peptides) is comprised of at least: A*0201, A*0202,A*0203, A*0204, A*0205, A*0206, A*0207, A*0209, A*0214, A*6802, andA*6901. Other allele-specific HLA molecules predicted to be members ofthe A2 superfamily are shown in Tables 4D and 6. As explained in detailbelow, binding to each of the individual allele-specific HLA moleculescan be modulated by substitutions at the primary anchor and/or secondaryanchor positions, preferably choosing respective residues specified forthe supermotif.

HLA-A*0201 Motif

An HLA-A2*0201 motif was determined to be characterized by the presencein peptide ligands of L or M as a primary anchor residue in position 2,and L or V as a primary anchor residue at the C-terminal position of a9-residue peptide (see, e.g., Falk et al., Nature 351:290-296 (1991))and was further found to comprise an I at position 2 and I or A at theC-terminal position of a nine amino acid peptide (see, e.g., Hunt etal., Science 255:1261-1263, Mar. 6, 1992; Parker et al., J. Immunol.149:3580-3587 (1992)) and position 10 of a decamer peptide. The A*0201allele-specific motif has also been defined by the present inventors toadditionally comprise V, A, T, or Q as a primary anchor residue atposition 2, and M or T as a primary anchor residue at the C-terminalposition of the epitope (see, e.g., Kast et al., J. Immunol.152:3904-3912, 1994).

Thus, the HLA-A*0201 motif comprises peptide ligands with L, I, V, M, A,T, or Q as primary anchor residues at position 2 and L, I, V, M, A, or Tas a primary anchor residue at the C-terminal position of the epitope.For this motif-supermotif relationship the preferred and lesspreferred/tolerated residues that characterize the primary anchorpositions of the HLA-A*0201 motif are identical to the residuesdescribing the A2 supermotif. (For reviews of relevant data, see, e.g.,del Guercio et at., J. Immunol. 154:685-693, 1995; Ruppert et al., Cell74:929-937, 1993; Sidney et al., Immunol. Today 17:261-266, 1996; Setteand Sidney, Curr. Opin. in Immunol. 10:478-482, 1998). Secondary anchorresidues that characterize the A*0201 motif have additionally beendefined (see, e.g., Ruppert et al., Cell 74:929-937, 1993). Thesesecondary anchors are shown in Tables 4A, 4B, and 4C. Peptide binding toHLA-A*0201 molecules can be modulated by substitutions at primary and/orsecondary anchor positions, preferably choosing respective residuesspecified for the motif.

Motifs Indicative of Class II HTL Inducing Peptide Epitopes

The primary and secondary anchor residues of the HLA class II peptideepitope supermotifs and motifs are summarized in U.S. Pat. Nos.5,736,142, 5,679,640 and 6,413,935; co-pending applications entitledAlteration Of Immune Responses Using Pan DR Binding Peptides, U.S. Ser.No. 09/709,774, filed Nov. 8, 2000 and 09/707,738, filed Nov. 6, 2000;and PCT publication Nos. WO 95/07707 and WO 97/26784.

Immune Response-Stimulating Peptide Analogs

In general, CTL and HTL responses are not directed against all possibleepitopes. Rather, they are restricted to a few “immunodominant”determinants (Zinkemagel, et al., Adv. Immunol. 27:5159, 1979; Bennink,et al., J. Exp. Med. 168:19351939, 1988; Rawle, et al., J. Immunol.146:3977-3984, 1991). It has been recognized that immunodominance(Benacerraf, et al., Science 175:273-279, 1972) could be explained byeither the ability of a given epitope to selectively bind a particularHLA protein (determinant selection theory) (Vitiello, et al., J.Immunol. 131:1635, 1983); Rosenthal, et al., Nature 267:156-158, 1977),or to be selectively recognized by the existing TCR (T cell receptor)specificities (repertoire theory) (Klein, J., IMMUNOLOGY, THE SCIENCE OFSELFNONSELF DISCRIMINATION, John Wiley & Sons, New York, pp. 270-310,1982). It has been demonstrated that additional factors, mostly linkedto processing events, can also play a key role in dictating, beyondstrict immunogenicity, which of the many potential determinants will bepresented as immunodominant (Sercarz, et al., Annu. Rev. Immunol.11:729-766, 1993).

The concept of dominance and subdominance is relevant to immunotherapyof both infectious diseases and malignancies. For example, in the courseof chronic viral disease, recruitment of subdominant epitopes can beimportant for successful clearance of the infection, especially ifdominant CTL or HTL specificities have been inactivated by functionaltolerance, suppression, mutation of viruses and other mechanisms(Franco, et al., Curr. Opin. Immunol. 7:524-531, 1995). In the case ofcancer and tumor antigens, CTLs recognizing at least some of the highestbinding affinity peptides might be functionally inactivated. Lowerbinding affinity peptides are preferentially recognized at these times,and may therefore be preferred in therapeutic or prophylacticanti-cancer vaccines.

In particular, it has been noted that a significant number of epitopesderived from known non-viral tumor associated antigens (TAA) bind HLAclass I with intermediate affinity (IC₅₀ in the 50-500 nM range) ratherthan at high affinity (IC₅₀ of less than 50 nM).

For example, it has been found that 8 of 15 known TAA peptidesrecognized by tumor infiltrating lymphocytes (TEL) or CTL bound in the50-500 nM range. (These data are in contrast with estimates that 90% ofknown viral antigens were bound by HLA class I molecules with IC₅₀ of 50nM or less, while only approximately 10% bound in the 50-500 nM range(Sette, et al., J. Immunol., 153:558-592, 1994). In the cancer settingthis phenomenon is probably due to elimination or functional inhibitionof the CTL recognizing several of the highest binding peptides,presumably because of T cell tolerization events.

Without intending to be bound by theory, it is believed that because Tcells to dominant epitopes may have been clonally deleted, and selectingsubdominant epitopes may allow existing T cells to be recruited, whichwill then lead to a therapeutic or prophylactic response. However, thebinding of HLA molecules to subdominant epitopes is often less vigorousthan to dominant ones.

Accordingly, there is a need to be able to modulate the binding affinityof particular immunogenic epitopes for one or more HLA molecules, tothereby modulate the immune response elicited by the peptide, forexample to prepare analog peptides which elicit a more vigorousresponse. This ability to modulate both binding affinity and theresulting immune response in accordance with the present inventiongreatly enhances the usefulness of peptide epitope-based vaccines andtherapeutic agents.

Although peptides with suitable cross-reactivity among all alleles of asuperfamily are identified by the screening procedures described above,cross-reactivity is not always as complete as possible, and in certaincases procedures to increase cross-reactivity of peptides can be useful;moreover, such procedures can also be used to modify other properties ofthe peptides such as binding affinity or peptide stability. Havingestablished the general rules that govern cross-reactivity of peptidesfor HLA alleles within a given motif or supermotif, modification (i.e.,analoging) of the structure of peptides of particular interest in orderto achieve broader (or otherwise modified) HLA binding capacity can beperformed. More specifically, peptides that exhibit the broadestcross-reactivity patterns, can be produced in accordance with theteachings herein. The present concepts related to analog generation areset forth in greater detail in co-pending U.S. Ser. No. 09/226,775 filed6 Jan. 1999.

In brief, the analoging strategy utilizes the motifs or supermotifs thatcorrelate with binding to certain HLA molecules. Analog peptides can becreated by substituting amino acid residues at primary anchor, secondaryanchor, or at primary and secondary anchor positions. Generally, analogsare made for peptides that already bear a motif or supermotif. As notedherein, preferred primary and secondary anchor residues of supermotifsand motifs for HLA-A2 class I binding peptides are shown in Tables 4A,4B, and 4C. For a number of the motifs or supermotifs in accordance withthe invention, residues are defined which are deleterious to binding toallele-specific HLA molecules or members of HLA supertypes that bind therespective motif or supermotif (Table 4C). Accordingly, removal of suchresidues that are detrimental to binding can be performed in accordancewith the present invention.

Thus, one strategy to improve the cross-reactivity of peptides within agiven supermotif is simply to delete one or more of the deleteriousresidues present within a peptide and substitute a small “neutral”residue such as Ala (that may not influence T cell recognition of thepeptide). An enhanced likelihood of cross-reactivity is expected if,together with elimination of detrimental residues within a peptide,“preferred” residues associated with high affinity binding to anallele-specific HLA molecule or to multiple HLA molecules within asuperfamily are inserted.

To ensure that an analog peptide, when used as a vaccine, actuallyelicits a CTL response to the native epitope in vivo (or, in the case ofclass II epitopes, elicits helper T cells that cross-react with the wildtype peptides), the analog peptide may be used to induce T cells invitro from individuals of the appropriate HLA allele. Thereafter, theimmunized cells' capacity to lyse wild type peptide sensitized targetcells is evaluated. Alternatively, evaluation of the cells' activity canbe evaluated by monitoring IFN release. Each of these cell monitoringstrategies evaluate the recognition of the APC by the CTL. It will bedesirable to use as antigen presenting cells, cells that have beeneither infected, or transfected with the appropriate genes, or,(generally only for class II epitopes, due to the different peptideprocessing pathway for HLA class II), cells that have been pulsed withwhole protein antigens, to establish whether endogenously producedantigen is also recognized by the T cells induced by the analog peptide.It is to be noted that peptide/protein-pulsed dendritic cells can beused to present whole protein antigens for both HLA class I and class U.

Another embodiment of the invention is to create analogs of weak bindingpeptides, to thereby ensure adequate numbers of cellular binders. ClassI binding peptides exhibiting binding affinities of 500-5000 nM, andcarrying an acceptable but suboptimal primary anchor residue at one orboth positions can be “fixed” by substituting preferred anchor residuesin accordance with the respective supertype. The analog peptides canthen be tested for binding and/or cross-binding capacity.

Another embodiment of the invention is to create analogs of peptidesthat are already cross-reactive binders and are vaccine candidates, butwhich bind weakly to one or more alleles of a supertype. If thecross-reactive binder carries a suboptimal residue (less preferred ordeleterious) at a primary or secondary anchor position, the peptide canbe analoged by substituting out a deleterious residue and replacing itwith a preferred or less preferred one, or by substituting out a lesspreferred reside and replacing it with a preferred one. The analogpeptide can then be tested for cross-binding capacity.

Another embodiment for generating effective peptide analogs involves thesubstitution of residues that have an adverse impact on peptidestability or solubility in, e.g., a liquid environment. Thissubstitution may occur at any position of the peptide epitope. Forexample, a cysteine (C) can be substituted in favor of α-amino butyricacid. Due to its chemical nature, cysteine has the propensity to formdisulfide bridges and sufficiently alter the peptide structurally so asto reduce binding capacity. Substituting α-amino butyric acid for C notonly alleviates this problem, but actually improves binding andcrossbinding capability in certain instances (see, e.g., the review bySette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I.Chen, John Wiley & Sons, England, 1999). Substitution of cysteine withα-amino butyric acid may occur at any residue of a peptide epitope, i.e.at either anchor or non-anchor positions.

Moreover, it has been shown that in sets of A*0201 motif-bearingpeptides containing at least one preferred secondary anchor residuewhile avoiding the presence of any deleterious secondary anchorresidues, 69% of the peptides will bind A*0201 with an IC₅₀ less than500 nM (Ruppert, J. et al. Cell 74:929, 1993). The determination of whatwas a preferred or deleterious residue in Ruppert can be used togenerate algorithms. Such algorithms are flexible in that cut-off scoresmay be adjusted to select sets of peptides with greater or lowerpredicted binding properties, as desired.

In accordance with the procedures described herein, tumor associatedantigen peptide epitopes and analogs thereof that were found to bindHLA-A2 allele-specific molecules and to bind members of the HLA-A2supertype have been identified.

Furthermore, additional amino acid residues can be added to the terminiof a peptide to provide for ease of linking peptides one to another, forcoupling to a carrier support or larger peptide, for modifying thephysical or chemical properties of the peptide or oligopeptide, or thelike. Amino acid residues such as tyrosine, cysteine, lysine, glutamicor aspartic acid, or any naturally occurring or any non-naturallyoccurring amino acid residues, can be introduced at the C- and/orN-terminus of the peptide or oligopeptide, particularly class Ipeptides. It is to be noted that modification at the carboxyl terminusof a CTL epitope may, in some cases, alter binding characteristics ofthe peptide. In addition, the peptide or oligopeptide sequences candiffer from the natural sequence by being modified by terminal-NH₂acylation, e.g., by alkanoyl (C₁-C₂₀) or thioglycolyl acetylation,terminal-carboxyl amidation, e.g., ammonia, methylamine etc. In someinstances these modifications may provide sites for linking to a supportor other molecule.

Assays to Detect T-Cell Responses

Once HLA binding peptides are identified, they can be tested for theability to elicit a T-cell response. The preparation and evaluation ofmotif-bearing peptides are described, e.g., in PCT publications WO94/20127 and WO 94/03205. Briefly, peptides comprising epitopes from aparticular antigen are synthesized and tested for their ability to bindto relevant HLA proteins. These assays may involve evaluation of peptidebinding to purified HLA class I molecules in relation to the binding ofa radioiodinated reference peptide. Alternatively, cells expressingempty class I molecules (i.e. cell surface HLA molecules that lack anybound peptide) may be evaluated for peptide binding by immunofluorescentstaining and flow microfluorimetry. Other assays that may be used toevaluate peptide binding include peptide-dependent class I assemblyassays and/or the inhibition of CTL recognition by peptide competition.Those peptides that bind to an HLA class I molecule, typically with anaffinity of 500 nM or less, are further evaluated for their ability toserve as targets for CTLs derived from infected or immunizedindividuals, as well as for their capacity to induce primary in vitro orin vivo CTL responses that can give rise to CTL populations capable ofreacting with selected target cells associated with pathology.

Analogous assays are used for evaluation of HLA class II bindingpeptides. HLA class II motif-bearing peptides that are shown to bind,typically at an affinity of 1000 nM or less, are further evaluated forthe ability to stimulate HTL responses.

Conventional assays utilized to detect T cell responses includeproliferation assays, lymphokine secretion assays, direct cytotoxicityassays, and limiting dilution assays. For example, antigen-presentingcells that have been incubated with a peptide can be assayed for theability to induce CTL responses in responder cell populations.Antigen-presenting cells can be normal cells such as peripheral bloodmononuclear cells or dendritic cells. Alternatively, mutant, non-humanmammalian cell lines that have been transfected with a human class I MHCgene, and that are deficient in their ability to load class I moleculeswith internally processed peptides, are used to evaluate the capacity ofthe peptide to induce in vitro primary CTL responses. Peripheral bloodmononuclear cells (PBMCs) can be used as the source of CTL precursors.Antigen presenting cells are incubated with peptide, after which thepeptide-loaded antigen-presenting cells are then incubated with theresponder cell population under optimized culture conditions. PositiveCTL activation can be determined by assaying the culture for thepresence of CTLs that lyse radio-labeled target cells, either specificpeptide-pulsed targets or target cells that express endogenouslyprocessed antigen from which the specific peptide was derived.Alternatively, the presence of epitope-specific CTLs can be determinedby IFNγ in situ ELISA.

In an embodiment of the invention, directed to diagnostics, a method hasbeen devised which allows direct quantification of antigen-specific Tcells by staining with fluorescein-labelled HLA tetrameric complexes(Altman, J. D. et al., Proc. Natl. Acad. Sci. USA 90:10330, 1993;Altman, J. D. et al., Science 274:94, 1996). Other options includestaining for intracellular lymphokines, and interferon release assays orELISPOT assays. Tetramer staining, intracellular lymphokine staining andELISPOT assays all appear to be at least 10-fold more sensitive thanmore conventional assays (Lalvani, A. et al., J. Exp. Med. 186:859,1997; Dunbar, P. R. et Curr. Biol. 8:413, 1998; Murali-Krishna, K. etal., Immunity 8:177, 1998). Additionally, DimerX technology can be usedas a means of quantitation (see, e.g., Science 274:94-99 (1996) andProc. Natl. Acad. Sci. 95:7568-73 (1998)).

HTL activation may also be assessed using techniques known to those inthe art, such as T cell proliferation or lymphokine secretion (see, e.g.Alexander et al., Immunity 1:751-761, 1994).

Alternatively, immunization of HLA transgenic mice can be used todetermine immunogenicity of peptide epitopes. Several transgenic mousestrains, e.g., mice with human A2.1, A11 (which can additionally be usedto analyze HLA-A3 epitopes), and B7 alleles have been characterized.Other transgenic mice strains (e.g., transgenic mice for HLA A1 and A24)are being developed. Moreover, HLA-DR1 and HLA-DR3 mouse models havebeen developed. In accordance with principles in the art, additionaltransgenic mouse models with other HLA alleles are generated asnecessary.

Such mice can be immunized with peptides emulsified in IncompleteFreund's Adjuvant; thereafter any resulting T cells can be tested fortheir capacity to recognize target cells that have been peptide-pulsedor transfected with genes encoding the peptide of interest. CTLresponses can be analyzed using cytotoxicity assays described above.Similarly, HTL responses can be analyzed using, e.g., T cellproliferation or lymphokine secretion assays.

Minigenes

A number of different approaches are available which allow simultaneousdelivery of multiple epitopes. Nucleic acids encoding multiple epitopesare a useful embodiment of the invention; discrete peptide epitopes orpolyepitopic peptides can be encoded. The epitopes to be included in aminigene are preferably selected according to the guidelines set forthin the previous section. Examples of amino acid sequences that can beincluded in a minigene include: HLA class I epitopes, HLA class IIepitopes, a ubiquitination signal sequence, and/or a targeting sequencesuch as an endoplasmic reticulum (ER) signal sequence to facilitatemovement of the resulting peptide into the endoplasmic reticulum.

The use of multi-epitope minigenes is also described in, e.g.,co-pending applications U.S. Ser. No. 09/311,784, 09/894,018,60/419,973, 60/415,463; Ishioka et al., J. Immunol. 162:3915-3925, 1999;An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. etal., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348,1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, amulti-epitope DNA plasmid encoding nine dominant HLA-A*0201- andA11-restricted CTL epitopes derived from the polymerase, envelope, andcore proteins of HBV and human immunodeficiency virus (HIV), a PADRE®universal helper T cell (HTL) epitope, and an endoplasmicreticulum-translocating signal sequence has been engineered.Immunization of HLA transgenic mice with this plasmid construct resultedin strong CTL induction responses against the nine CTL epitopes tested.This CTL response was similar to that observed with a lipopeptide ofknown immunogenicity in humans, and significantly greater thanimmunization using peptides in oil-based adjuvants. Moreover, theimmunogenicity of DNA-encoded epitopes in vitro was also correlated withthe in vitro responses of specific CTL lines against target cellstransfected with the DNA plasmid. These data show that the minigeneserved: 1.) to generate a CTL response and 2.) to generate CTLs thatrecognized cells expressing the encoded epitopes. A similar approach canbe used to develop minigenes encoding TAA epitopes.

For example, to create a DNA sequence encoding the selected epitopes(minigene) for expression in human cells, the amino acid sequences ofthe epitopes may be reverse translated. A human codon usage table can beused to guide the codon choice for each amino acid. Theseepitope-encoding DNA sequences may be directly adjoined, so that whentranslated, a continuous peptide sequence is created. However, tooptimize expression and/or immunogenicity, additional elements can beincorporated into the minigene design such as spacer amino acid residuesbetween epitopes. HLA presentation of CTL and HTL epitopes may beimproved by including synthetic (e.g. poly-alanine) ornaturally-occurring flanking sequences adjacent to the CTL or HTLepitopes; these larger peptides comprising the epitope(s) are within thescope of the invention. In one embodiment, spacer amino acid residuesbetween one or more CTL and/or HTL epitopes are designed so as tominimize junctional epitopes that may result from the juxtaposition of 2CTL and/or HTL epitopes.

The minigene sequence may be converted to DNA by assemblingoligonucleotides that encode the plus and minus strands of the minigene.Overlapping oligonucleotides (30-100 bases long) may be synthesized,phosphorylated, purified and annealed under appropriate conditions usingwell known techniques. The ends of the oligonucleotides can be joined,for example, using T4 DNA ligase. This synthetic minigene, encoding theepitope peptide, can then be cloned into a desired expression vector.

Standard regulatory sequences well known to those of skill in the artare preferably included in the vector to ensure expression in the targetcells. Several vector elements are desirable: a promoter with adownstream cloning site for minigene insertion; a polyadenylation signalfor efficient transcription termination; an E. coli origin ofreplication; and an E. coli selectable marker (e.g. ampicillin orkanamycin resistance). Numerous promoters can be used for this purpose,e.g., the human cytomegalovirus (hCMV) CMV-IE promoter. See, e.g., U.S.Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Optimized peptide expression and immunogenicity can be achieved bycertain modifications to a minigene construct. For example, in somecases introns facilitate efficient gene expression, thus one or moresynthetic or naturally-occurring introns can be incorporated into thetranscribed region of the minigene. The inclusion of mRNA stabilizationsequences and sequences for replication in mammalian cells may also beconsidered for increasing minigene expression.

Once an expression vector is selected, the minigene is cloned into thepolylinker region downstream of the promoter. This plasmid istransformed into an appropriate bacterial strain, and DNA is preparedusing standard techniques. The orientation and DNA sequence of theminigene, as well as all other elements included in the vector, areconfirmed using restriction mapping, PCR and/or DNA sequence analysis.Bacterial cells harboring the correct plasmid can be stored as cellbanks.

In addition, immunostimulatory sequences (ISSs or CpGs) appear to play arole in the immunogenicity of DNA vaccines. These sequences may beincluded in the vector, outside the minigene coding sequence to enhanceimmunogenicity.

In some embodiments, a bi-cistronic expression vector which allowsproduction of both the minigene-encoded epitopes and a second protein(e.g., one that modulates immunogenicity) can be used. Examples ofproteins or polypeptides that, if co-expressed with epitopes, canenhance an immune response include cytokines (e.g., IL-2, IL-12,GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatorymolecules, or pan-DR binding proteins (PADRE®, Epimmune, San Diego,Calif.). Helper T cell (HTL) epitopes such as PADRE® molecules can bejoined to intracellular targeting signals and expressed separately fromexpressed CTL epitopes. This can be done in order to direct HTL epitopesto a cell compartment different than that of the CTL epitopes, one thatprovides for more efficient entry of HTL epitopes into the HLA class IIpathway, thereby improving HTL induction. In contrast to HTL or CTLinduction, specifically decreasing the immune response by co-expressionof immunosuppressive molecules (e.g. TGF-β) may be beneficial in certaindiseases.

Therapeutic quantities of plasmid DNA can be produced for example, byfermentation in E. coli, followed by purification. Aliquots from theworking cell bank are used to inoculate growth medium, and are grown tosaturation in shaker flasks or a bioreactor according to well knowntechniques. Plasmid DNA is purified using standard bioseparationtechnologies such as solid phase anion-exchange resins available, e.g.,from QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA canbe isolated from the open circular and linear forms using gelelectrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety offormulations. The simplest of these is reconstitution of lyophilized DNAin sterile phosphate buffer saline (PBS). This approach, known as “nakedDNA,” is currently being used for intramuscular (IM) administration inclinical trials. To maximize the immunotherapeutic effects of minigenevaccines, alternative methods of formulating purified plasmid DNA may beused. A variety of such methods have been described, and new techniquesmay become available. Cationic lipids, glycolipids, and fusogenicliposomes can also be used in the formulation (see, e.g., WO 93/24640;Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No.5,279,833; WO 91/06309; and Feigner, et al., Proc. Nat'l Acad. Sci. USA84:7413 (1987). In addition, peptides and compounds referred tocollectively as protective, interactive, non-condensing compounds (PINC)can also be complexed to purified plasmid DNA to influence variablessuch as stability, intramuscular dispersion, or trafficking to specificorgans or cell types.

Known methods in the art can be used to enhance delivery and uptake of apolynucleotide in vivo. For example, the polynucleotide can be complexedto polyvinylpyrrolidone (PVP), to prolong the localized bioavailabilityof the polynucleotide, thereby enhancing uptake of the polynucleotide bythe organisum (see e.g., U.S. Pat. No. 6,040,295; EP 0 465 529; WO98/17814). PVP is a polyamide that is known to form complexes with awide variety of substances, and is chemically and physiologically inert.

Target cell sensitization can be used as a functional assay of theexpression and HLA class I presentation of minigene-encoded epitopes.For example, the plasmid DNA is introduced into a mammalian cell linethat is a suitable target for standard CTL chromium release assays. Thetransfection method used will be dependent on the final formulation,electroporation can be used for “naked” DNA, whereas cationic lipids orDNA:PVP compositions allow direct in vitro transfection. A plasmidexpressing green fluorescent protein (GFP) can be co-transfected toallow enrichment of transfected cells using fluorescence activated cellsorting (FACS). The transfected cells are then chromium-51 (⁵¹Cr)labeled and used as targets for epitope-specific CTLs. Cytolysis of thetarget cells, detected by ⁵¹Cr release, indicates both the productionand HLA presentation of, minigene-encoded CTL epitopes. Expression ofHTL epitopes may be evaluated in an analogous manner using assays toassess HTL activity.

In vivo immunogenicity is a second approach for functional testing ofminigene DNA formulations. Transgenic mice expressing appropriate humanHLA proteins are immunized with the DNA product. The dose and route ofadministration are formulation dependent (e.g., IM for DNA in PBS,intraperitoneal (IP) for lipid-complexed DNA). Eleven to twenty-one daysafter immunization, splenocytes are harvested and restimulated for oneweek in the presence of peptides encoding each epitope being tested.Thereafter, for CTLs, standard assays are conducted to determine ifthere is cytolysis of peptide-loaded, ⁵¹Cr-labeled target cells. Onceagain, lysis of target cells that were exposed to epitopes correspondingto those in the minigene, demonstrates DNA vaccine function andinduction of CTLs. Immunogenicity of HTL epitopes is evaluated intransgenic mice in an analogous manner.

Alternatively, the nucleic acids can be administered using ballisticdelivery as described, for instance, in U.S. Pat. No. 5,204,253. Usingthis technique, particles comprised solely of DNA are administered. In afurther alternative embodiment for ballistic delivery, DNA can beadhered to particles, such as gold particles.

Vaccine Compositions

Vaccines that contain an immunologically effective amount of one or morepeptides or polynucleotides of the invention are a further embodiment ofthe invention. The peptides can be delivered by various means orformulations, all collectively referred to as “vaccine” compositions.Such vaccine compositions, and/or modes of administration, can include,for example, naked DNA, DNA formulated with PVP, DNA in cationic lipidformulations; lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest.95:341, 1995), DNA or peptides, encapsulated e.g., inpoly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge,et al., Molec. Inzmunol. 28:287-294, 1991: Alonso et al., Vaccine12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995); peptidecompositions contained in immune stimulating complexes (ISCOMS) (see,e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin ExpImmunol. 113:235-243, 1998); multiple antigen peptide systems (MAPS)(see e.g., Tarn, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413,1988; Tam, J. P J. Immunol. Methods 196:17-32, 1996); viral, bacterial,or, fungal delivery vectors (Perkus, M. E. et al., In: Concepts invaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti,S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986;Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al.,J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535,1990); particles of viral or synthetic origin (e.g., Kofler, N. et al,J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem.Henzatol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649,1995); adjuvants (e.g., incomplete freund's advjuvant) (Warren, H. S.,Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta,R. K. et al., Vaccine 11:293, 1993); liposomes (Reddy, R. et al., J.Immunol. 148:1585, 1992; Rock, K. L., Immunol Today 17:131, 1996); or,particle-absorbed DNA (Ulmer, J. B. et al., Science 259:1745, 1993;Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993;Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S.H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev.Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16,1993), etc. Toxin-targeted delivery technologies, also known as receptormediated targeting, such as those of Avant Immunotherapeutics, Inc.(Needham, Mass.) or attached to a stress protein, e.g., HSP 96(Stressgen Biotechnologies Corp., Victoria, BC, Canada) can also beused.

Vaccines of the invention comprise nucleic acid mediated modalities. DNAor RNA encoding one or more of the peptides of the invention can beadministered to a patient. This approach is described, for instance, inWolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos.5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; and,WO 98/04720. Examples of DNA-based delivery technologies include “nakedDNA”, facilitated ((i.e., non-“naked DNA”) e.g., facilitated bycombination with bupivicaine, polymers (e.g., PVP), peptide-mediated)delivery, cationic lipid complexes, and particle-mediated (“gene gun”)or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).Accordingly, peptide vaccines of the invention can be expressed by viralor bacterial vectors. Examples of expression vectors include attenuatedviral hosts, such as vaccinia or fowlpox. For example, vaccinia virus isused as a vector to express nucleotide sequences that encode thepeptides of the invention (e.g., MVA). Upon introduction into an acutelyor chronically infected host or into a non-infected host, therecombinant vaccinia virus expresses the immunogenic peptide, andthereby elicits an immune response. Vaccinia vectors and methods usefulin immunization protocols are described in, e.g., U.S. Pat. No.4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectorsare described in Stover et al., Nature 351:456-460 (1991). A widevariety of other vectors useful for therapeutic administration orimmunization of the peptides of the invention, e.g. adeno andadeno-associated virus vectors, alpha virus vectors, retroviral vectors,Salmonella typhi vectors, detoxified anthrax toxin vectors, and thelike, are apparent to those skilled in the art from the descriptionherein.

Furthermore, vaccines in accordance with the invention can comprise oneor more peptides of the invention. Accordingly, a peptide can be presentin a vaccine individually; alternatively, the peptide can exist as ahomopolymer comprising multiple copies of the same peptide, or as aheteropolymer of various peptides. Polymers have the advantage ofincreased probability for immunological reaction and, where differentpeptide epitopes are used to make up the polymer, the ability to induceantibodies and/or T cells that react with different antigenicdeterminants of the antigen targeted for an immune response. Thecomposition may be a naturally occurring region of an antigen or can beprepared, e.g., recombinantly or by chemical synthesis.

Carriers that can be used with vaccines of the invention are well knownin the art, and include, e.g., thyroglobulin, albumins such as humanserum albumin, tetanus toxoid, polyamino acid residues such as polyL-lysine, poly L-glutamic acid, influenza virus proteins, hepatitis Bvirus core protein, and the like The vaccines can contain aphysiologically tolerable diluent such as water, or a saline solution,preferably phosphate buffered saline. Generally, the vaccines alsoinclude an adjuvant. Adjuvants such as incomplete Freund's adjuvant,aluminum phosphate, aluminum hydroxide, or alum are examples ofmaterials well known in the art. Additionally, as disclosed herein, CTLresponses can be primed by conjugating peptides of the invention tolipids, such as tripalmitoyl-S-glyceryl-cysteinyl-seryl-serine (P₃CSS).

Upon immunization with a peptide composition in accordance with theinvention, via injection (e.g., SC, ID, IM), aerosol, oral, transdermal,transmucosal, intrapleural, intrathecal, or other suitable routes, theimmune system of the host responds to the vaccine by producingantibodies, CTLs and/or HTLs specific for the desired antigen.Consequently, the host becomes at least partially immune to subsequentexposure to the TAA, or at least partially resistant to furtherdevelopment of TAA-bearing cells and thereby derives a prophylactic ortherapeutic benefit

In certain embodiments, components that induce T cell responses arecombined with components that induce antibody responses to the targetantigen of interest. A preferred embodiment of such a compositioncomprises class I and class II epitopes in accordance with theinvention. Alternatively, a composition comprises a class I and/or classII epitope in accordance with the invention, along with a PADRE®molecule (Epimmune, San Diego, Calif.).

Vaccines of the invention can comprise antigen presenting cells, such asdendritic cells, as a vehicle to present peptides of the invention. Forexample, dendritic cells are transfected, e.g., with a minigeneconstruct in accordance with the invention, in order to elicit immuneresponses. Minigenes are discussed in greater detail in a followingsection. Vaccine compositions can be created in vitro, followingdendritic cell mobilization and harvesting, whereby loading of dendriticcells occurs in vitro.

The vaccine compositions of the invention may also be used incombination with antiviral drugs such as interferon-α, or immuneadjuvants such as IL-12, GM-CSF, etc.

Preferably, the following principles are utilized when selectingepitope(s) and/or analogs for inclusion in a vaccine, either peptidebased or nucleic acid-based formulations. Exemplary epitopes and analogsthat may be utilized in a vaccine to treat or prevent TAA-associateddisease are set out in Table 3. Each of the following principles can bebalanced in order to make the selection. When multiple epitopes are tobe used in a vaccine, the epitopes may be, but need not be, contiguousin sequence in the native antigen from which the epitopes are derived.Such multiple epitotes can refer to the order of epitopes within apeptide, or to the selection of epitopes that come from the samereagion, for use in either individual peptides or in a multi-epitopicpeptide.

1.) Epitopes and/or analogs are selected which, upon administration,mimic immune responses that have been observed to be correlated withprevention or clearance of TAA-expressing tumors. For HLA Class I, thisgenerally includes 34 epitopes and/or analogs from at least one TAA.

2.) Epitopes and/or analogs are selected that have the requisite bindingaffinity established to be correlated with immunogenicity: for HLA ClassI an IC₅₀ of 500 nM or less, or for Class II an IC₅₀ of 1000 nM or less.For HLA Class I it is presently preferred to select a peptide having anIC₅₀ of 200 nM or less, as this is believed to better correlate not onlyto induction of an immune response, but to in vitro tumor cell killingas well. For HLA A1 and A24, it is especially preferred to select apeptide having an IC₅₀ of 100 nM or less.

3.) Supermotif bearing-epitopes and/or analogs, or a sufficient array ofallele-specific motif-bearing epitopes and/or analogs, are selected togive broad population coverage. In general, it is preferable to have atleast 80% population coverage. A Monte Carlo analysis, a statisticalevaluation known in the art, can be employed to assess the breadth ofpopulation coverage.

4.) For cancer-related antigens, it can be preferable to select analogsinstead of or in addition to epitopes, because the patient may havedeveloped tolerance to the native epitope.

5.) Of particular relevance are “nested epitopes.” Nested epitopes occurwhere at least two epitopes overlap in a given peptide sequence. Forexample, a nested epitope can be a fragment of an antigen from a regionthat contains multiple epitopes that are overleapping, or one epitopethat is completely encompassed by another, e.g., A2 peptides MAGE3.159and MAGE3.160 are nested. A peptide comprising “transcendent nestedepitopes” is a peptide that has both HLA class I and HLA class IIepitopes in it. When providing nested epitopes, it is preferable toprovide a sequence that has the greatest number of epitopes per providedsequence. Preferably, one avoids providing a peptide that is any longerthan the amino terminus of the amino terminal epitope and the carboxylterminus of the carboxyl terminal epitope in the peptide. When providinga sequence comprising nested epitopes, it is important to evaluate thesequence in order to insure that it does not have pathological or otherdeleterious biological properties; this is particularly relevant forvaccines directed to infectious organisms.

6.) If a protein with multiple epitopes or a polynucleotide (e.g.,minigene) is created, an objective is to generate the smallest peptidethat encompasses the epitopes of interest. This principle is similar, ifnot the same as that employed when selecting a peptide comprising nestedepitopes. However, with an artificial peptide comprising multipleepitopes, the size minimization objective is balanced against the needto integrate any spacer sequences between epitopes in the polyepitopicprotein. Spacer amino acid residues can be introduced to avoidjunctional epitopes (an epitope recognized by the immune system, notpresent in the target antigen, and only created by the man-madejuxtaposition of epitopes), or to facilitate cleavage between epitopesand thereby enhance epitope presentation. Junctional epitopes aregenerally to be avoided because the recipient may generate an immuneresponse to that non-native epitope. Of particular concern is ajunctional epitope that is a “dominant epitope.” A dominant epitope maylead to such a zealous response that immune responses to other epitopesare diminished or suppressed.

The principles are the same, except junctional epitopes applies to thesequences surrounding the epitope. One must also take care with othersequences in construct to avoid immune response.

T Cell Priming Materials

In some embodiments it may be desirable to include in the pharmaceuticalcompositions of the invention at least one component which primescytotoxic T lymphocytes. Lipids have been identified as agents capableof facilitating the priming in vitro-CTL response against viralantigens. For example, palmitic acid residues can be attached to the ε-and α-amino groups of a lysine residue and then linked to an immunogenicpeptide. One or more linking moieties can be used such as Gly, Gly-Gly-,Ser, Ser-Ser, or the like. The lipidated peptide can then beadministered directly in a micelle or particle, incorporated into aliposome, or emulsified in an adjuvant, e.g., incomplete Freund'sadjuvant. A preferred immunogenic composition comprises palmitic acidattached to ε- and α-amino groups of Lys via a linking moiety, e.g.,Ser-Ser, added to the amino terminus of an immunogenic peptide.

In another embodiment of lipid-facilitated priming of CTL responses, E.coli lipoproteins, such astripalmitoyl-S-glyceryl-cysteinyl-seryl-serine (P₃CSS) can be used toprime CTL when covalently attached to an appropriate peptide. (See,e.g., Deres, et al., Nature 342:561, 1989). Thus, peptides of theinvention can be coupled P₃CSS, and the lipopeptide administered to anindividual to specifically prime a CTL response to the target antigen.Moreover, because the induction of neutralizing antibodies can also beprimed with P₃CSS-conjugated epitopes, two such compositions can becombined to elicit both humoral and cell-mediated responses.

Dendritic Cells Pulsed with CTL and/or HTL Peptides

An embodiment of a vaccine composition in accordance with the inventioncomprises ex vivo administrations of a cocktail of epitope-bearingpeptides to PBMC, or isolated DC therefrom, from the patient's blood. Apharmaceutical to facilitate harvesting of DC can be used, such asProgenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/1L-4. After pulsingthe DC with peptides and prior to reinfusion into patients, the DC arewashed to remove unbound peptides. In this embodiment, a vaccinecomprises peptide-pulsed DCs which present the pulsed peptide epitopesin HLA molecules on their surfaces.

The DC can be pulsed ex vivo with a cocktail of peptides, some of whichstimulate CTL responses to one or more antigens of interest, e.g., tumorassociated antigens (TAA) such as HER2/neu, p53, MAGE 2, MAGE3, and/orcarcinoembryonic antigen (CEA). Collectively, these TAA are associatedwith breast, colon and lung cancers. Optionally, a helper T cell (HTL)peptide such as PADRE®, can be included to facilitate the CTL response.Thus, a vaccine in accordance with the invention comprising epitopesfrom HER2/neu, p53, MAGE 2, MAGE3, and carcinoembryonic antigen (CEA) isused to treat minimal or residual disease in patients with malignanciessuch as breast, colon, lung or ovarian cancer; any malignancies thatbear any of these TAAs can also be treated with the vaccine. A TAAvaccine can be used following debulking procedures such as surgery,radiation therapy or chemotherapy, whereupon the vaccine provides thebenefit of increasing disease free survival and overall survival in therecipients.

Thus, in preferred embodiments, a vaccine of the invention is a productthat treats a majority of patients across a number of different tumortypes. A vaccine comprising a plurality of epitopes, preferablysupermotif-bearing epitopes, offers such an advantage.

Diagnostic and Prognostic Uses

In one embodiment of the invention, HLA class I and class II bindingpeptides can be used as reagents to evaluate an immune response.Preferably, the following principles are utilized when selecting anepitope(s) and/or analog(s) for diagnostic, prognostic and similar uses.Potential principles include having the binding affinities describedearlier, and/or matching the HLA-motif/supermotif of a peptide with theHLA-type of a patient.

The evaluated immune response can be induced by any immunogen. Forexample, the immunogen may result in the production of antigen-specificCTLs or HTLs that recognize the peptide epitope(s) employed as thereagent. Thus, a peptide of the invention may or may not be used as theimmunogen. Assay systems that can be used for such analyses includetetramer-based protocols (e.g., DimerX technology (see, e.g., Science274:94-99 (1996) and Proc. Natl. Acad. Sci. 95:7568-73 (1998)), stainingfor intracellular lymphokines, interferon release assays, or ELISPOTassays.

For example, following exposure to a putative immunogen, a peptide ofthe invention can be used in a tetramer staining assay to assessperipheral blood mononuclear cells for the presence of anyantigen-specific CTLs. The HLA-tetrameric complex is used to directlyvisualize antigen-specific CTLs and thereby determine the frequency ofsuch antigen-specific CTLs in a sample of peripheral blood mononuclearcells (see, e.g., Ogg et al., Science 279:2103-2106, 1998; and Altman etal., Science 174:94-96, 1996).

A tetramer reagent comprising a peptide of the invention is generated asfollows: A peptide that binds to an HLA molecule is refolded in thepresence of the corresponding HLA heavy chain and β₂-microglobulin togenerate a trimolecular complex. The complex is biotinylated at thecarboxyl terminal end of the HLA heavy chain, at a site that waspreviously engineered into the protein. Tetramer formation is theninduced by adding streptavidin. When fluorescently labeled streptavidinis used, the tetrameric complex is used to stain antigen-specific cells.The labeled cells are then readily identified, e.g., by flow cytometry.Such procedures are used for diagnostic or prognostic purposes; thecells identified by the procedure can be used for therapeutic purposes.

Peptides of the invention are also used as reagents to evaluate immunerecall responses. (see, e.g., Bertoni et al., J. Clin. Invest.100:503-513, 1997 and Penna et al., J. Exp. Med. 174:1565-1570, 1991.)For example, a PBMC sample from an individual expressing adisease-associated antigen (e.g. a tumor-associated antigen such as CEA,p53, MAGE2/3,HER2neu, or an organism associated with neoplasia such asHPV or HSV) can be analyzed for the presence of antigen-specific CTLs orHTLs using specific peptides. A blood sample containing mononuclearcells may be evaluated by cultivating the PBMCs and stimulating thecells with a peptide of the invention. After an appropriate cultivationperiod, the expanded cell population may be analyzed, for example, forCTL or for HTL activity.

Thus, the peptides can be used to evaluate the efficacy of a vaccine.PBMCs obtained from a patient vaccinated with an immunogen may beanalyzed by methods such as those described herein. The patient is HLAtyped, and peptide epitopes that are bound by the HLA molecule(s)present in that patient are selected for analysis. The immunogenicity ofthe vaccine is indicated by the presence of CTLs and/or HTLs directed toepitopes present in the vaccine.

The peptides of the invention may also be used to make antibodies, usingtechniques well known in the art (see, e.g. CURRENT PROTOCOLS INIMMUNOLOGY, Wiley/Greene, NY; and Antibodies A Laboratory Manual Harlow,Harlow and Lane, Cold Spring Harbor Laboratory Press, 1989). Suchantibodies are useful as reagents to determine the presence ofdisease-associated antigens. Antibodies in this category include thosethat recognize a peptide when bound by an HLA molecule, i.e., antibodiesthat bind to a peptide-MHC complex.

Administration for Therapeutic or Prophylactic Purposes

The peptides and polynucleotides of the present invention, includingcompositions thereof, are useful for administration to mammals,particularly humans, to treat and/or prevent disease. In one embodiment,peptides, polynucleotides, or vaccine compositions (peptide or nucleicacid) of the invention are administered to a patient who has amalignancy associated with expression of one or more TAAs, or to anindividual susceptible to, or otherwise at risk for developingTAA-related disease. Upon administration an immune response is elicitedagainst the TAAs, thereby enhancing the patient's own immune responsecapabilities. In therapeutic applications, peptide and/or nucleic acidcompositions are administered to a patient in an amount sufficient toelicit an effective immune response to the TAA-expressing cells and tothereby cure, arrest or slow symptoms and/or complications. An amountadequate to accomplish this is defined as “therapeutically effectivedose.” Amounts effective for this use will depend on, e.g., theparticular composition administered, the manner of administration, thestage and severity of the disease being treated, the weight and generalstate of health of the patient, and the judgment of the prescribingphysician.

In certain embodiments, a method of treating cancer is provided. In somecases, the treatment of cancer may include the treatment of solid tumorsor the treatment of metastasis. Metastasis is the form of cancer whereinthe transformed or malignant cells are traveling and spreading thecancer from one site to another. The cancer can be of the colon,non-small cell lung cancer (“NSCLC”), the breast, the ovary, the kidney,the rectum, head and neck (including but not limited to the nasal andoral cavities), the prostate, the pancreas, small cell lung cancer, theuterus, the bladder, the thyroid, the skin (including, but not limitedto, malignant melanoma, basal cell carcinoma, squamous cell carcinoma,Karposi's sarcoma, moles dysplastic nevi, lipoma, angioma,dermatofibroma, keloids, psoriasis, and metastatic melanoma), breast,brain, cervical carcinomas, testicular carcinomas, etc. Moreparticularly, cancers may include, but are not limited to the followingorgans or systems: cardiac, lung, gastrointestinal, genitourinary tract,liver, bone, nervous system, gynecological, hematologic, skin, andadrenal glands. More particularly, the methods herein can be used fortreating gliomas (Schwannoma, glioblastoma, astrocytoma), neuroblastoma,pheochromocytoma, paraganlioma, meningioma, adrenalcortical carcinoma,kidney cancer, vascular cancer of various types, osteoblasticosteocarcinoma, prostate cancer, ovarian cancer, uterine leiomyomas,salivary gland cancer, choroid plexus carcinoma, mammary cancer,pancreatic cancer, colon cancer, and megakaryoblastic leukemia.

In preferred embodiments, the cancer to be treated by the presentinvention is colorectal cancer, non-small cell lung cancer (“NSCLC”),breast cancer, ovarian cancer, renal cancer, prostate cancer, cervicalcancer, head and/or neck cancer, endometrial cancer, pancreatic cancer,and/or esophageal cancer.

In preferred embodiments, the cancer to be treated by the presentinvention is colorectal cancer, non-small cell lung cancer (“NSCLC”),breast cancer, and/or ovarian cancer. In certain other preferredembodiments, the cancer is a cancer of the head and/or neck. The term“cancerous cell” as provided herein, includes a cell afflicted by anyone of the cancerous conditions provided herein, or any cancer.

In certain embodiments, the present invention may also be used to treatdiseases associated with increased cell survival, or the inhibition ofapoptosis, including cancers (such as follicular lymphomas, carcinomaswith p53 mutations, and hormone-dependent tumors, including, but notlimited to colon cancer, cardiac tumors, pancreatic cancer, melanoma,retinoblastoma, glioblastoma, lung cancer, intestinal cancer, testicularcancer, stomach cancer, neuroblastoma, myxoma, myoma, lymphoma,endothelioma, osteoblastoma, osteoclastoma, osteosarcoma,chondrosarcoma, adenoma, breast cancer, prostate cancer, Kaposi'ssarcoma and ovarian cancer); autoimmune disorders (such as, multiplesclerosis, Sjogren's syndrome, Hashimoto's thyroiditis, biliarycirrhosis, Behcet's disease, Crohn's disease, polymyositis, systemiclupus erythematosus and immune-related glomerulonephritis and rheumatoidarthritis) and viral infections (such as herpes viruses, pox viruses andadenoviruses), inflammation, graft v. host disease, acute graftrejection, and chronic graft rejection.

In certain embodiments, the invention is used to treat additionaldiseases or conditions associated with increased cell survivalincluding, but not limited to, progression, and/or metastases ofmalignancies and related disorders such as leukemia (including acuteleukemias (e.g., acute lymphocytic leukemia, acute myelocytic leukemia(including myeloblastic, promyelocytic, myelomonocytic, monocytic, anderythroleukemia)) and chronic leukemias (e.g., chronic myelocytic(granulocytic) leukemia and chronic lymphocytic leukemia)), polycythemiavera, lymphomas (e.g., Hodgkin's disease and non-Hodgkin's disease),multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease,and solid tumors including, but not limited to, sarcomas and carcinomassuch as fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma,osteogenic sarcoma, chordoma, angio sarcoma, endotheliosarcoma,lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma,Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma,pancreatic cancer, breast cancer, ovarian cancer, prostate cancer,squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweatgland carcinoma, sebaceous gland carcinoma, papillary carcinoma,papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma,bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile ductcarcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor,cervical cancer, testicular tumor, lung carcinoma, small cell lungcarcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma,medulloblastoma, craniopharyngioma, ependymoma, pinealoma,hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma,melanoma, neuroblastoma, and retinoblastoma.

The vaccine compositions of the invention can be used purely asprophylactic agents. Generally the dosage for an initial prophylacticimmunization generally occurs in a unit dosage range where the lowervalue is about 1, 5, 50, 500, or 1000 μg of peptide and the higher valueis about 10,000; 20,000; 30,000; or 50,000 μg of peptide. Dosage valuesfor a human typically range from about 500 μg to about 50,000 μg ofpeptide per 70 kilogram patient. This is followed by boosting dosages ofbetween about 1.0 μg to about 50,000 μg of peptide, administered atdefined intervals from about four weeks to six months after the initialadministration of vaccine. The immunogenicity of the vaccine may beassessed by measuring the specific activity of CTL and HTL obtained froma sample of the patient's blood.

As noted above, peptides comprising CTL and/or HTL epitopes of theinvention induce immune responses when presented by HLA molecules andcontacted with a CTL or HTL specific for an epitope comprised by thepeptide. The manner in which the peptide is contacted with the CTL orHTL is not critical to the invention. For instance, the peptide can becontacted with the CTL or HTL either in vitro or in vivo. If thecontacting occurs in vivo, peptide can be administered directly, or inother forms/vehicles, e.g., DNA vectors encoding one or more peptides,viral vectors encoding the peptide(s), liposomes, antigen presentingcells such as dendritic cells, and the like.

Accordingly, for pharmaceutical compositions of the invention in theform of peptides or polypeptides, the peptides or polypeptides can beadministered directly. Alternatively, the peptide/polypeptides can beadministered indirectly presented on APCs, or as DNA encoding them.Furthermore, the peptides or DNA encoding them can be administeredindividually or as fusions of one or more peptide sequences.

For therapeutic use, administration should generally begin at the firstdiagnosis of TAA-related disease. This is followed by boosting doses atleast until symptoms are substantially abated and for a periodthereafter. In chronic disease states, loading doses followed byboosting doses may be required.

The dosage for an initial therapeutic immunization generally occurs in aunit dosage range where the lower value is about 1, 5, 50, 500, or 1,000μg of peptide and the higher value is about 10,000; 20,000; 30,000; or50,000 μg of peptide. Dosage values for a human typically range fromabout 500 μg to about 50,000 μg of peptide per 70 kilogram patient.Boosting dosages of between about 1.0 μg to about 50,000 μg of peptide,administered pursuant to a boosting regimen over weeks to months, can beadministered depending upon the patient's response and condition.Patient response can be determined by measuring the specific activity ofCTL and HTL obtained from the patient's blood.

In certain embodiments, peptides and compositions of the presentinvention are used in serious disease states. In such cases, as a resultof the minimal amounts of extraneous substances and the relativenontoxic nature of the peptides, it is possible and may be desirable toadminister substantial excesses of these peptide compositions relativeto these stated dosage amounts.

For treatment of chronic disease, a representative dose is in the rangedisclosed above, namely where the lower value is about 1, 5, 50, 500, or1,000 μg of peptide and the higher value is about 10,000; 20,000;30,000; or 50,000 μg of peptide, preferably from about 500 μg to about50,000 μg of peptide per 70 kilogram patient. Initial doses followed byboosting doses at established intervals, e.g., from four weeks to sixmonths, may be required, possibly for a prolonged period of time toeffectively immunize an individual. In the case of chronic disease,administration should continue until at least clinical symptoms orlaboratory tests indicate that the disease has been eliminated orsubstantially abated, and for a follow-up period thereafter. Thedosages, routes of administration, and dose schedules are adjusted inaccordance with methodologies known in the art.

The pharmaceutical compositions for therapeutic treatment are intendedfor parenteral, topical, oral, intrathecal, or local administration.Preferably, the pharmaceutical compositions are administered parentally,e.g., intravenously, subcutaneously, intradermally, or intramuscularly.

Thus, in a preferred embodiment the invention provides compositions forparenteral administration which comprise a solution of the immunogenicpeptides dissolved or suspended in an acceptable carrier, preferably anaqueous carrier. A variety of aqueous carriers may be used, e.g., water,buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like.These compositions may be sterilized by conventional, well knownsterilization techniques, or may be sterile filtered. The resultingaqueous solutions may be packaged for use as is, or lyophilized, thelyophilized preparation being combined with a sterile solution prior toadministration. The compositions may contain pharmaceutically acceptableauxiliary substances or pharmaceutical excipients as may be required toapproximate physiological conditions, such as pH-adjusting and bufferingagents, tonicity adjusting agents, wetting agents, preservatives, andthe like, for example, sodium acetate, sodium lactate, sodium chloride,potassium chloride, calcium chloride, sorbitan monolaurate,triethanolamine oleate, etc.

The concentration of peptides of the invention in the pharmaceuticalformulations can vary widely, i.e., from less than about 0.1%, usuallyat or at least about 2% to as much as 20% to 50% or more by weight, andwill be selected primarily by fluid volumes, viscosities, etc., inaccordance with the particular mode of administration selected.

A human unit dose form of the peptide composition is typically includedin a pharmaceutical composition that also comprises a human unit dose ofan acceptable carrier, preferably an aqueous carrier, and isadministered in a volume of fluid that is known by those of skill in theart to be used for administration of such compositions to humans (see,e.g., Remington's Pharmaceutical Sciences, 17^(th) Edition, A. Gennaro,Editor, Mack Publishing Co., Easton, Pa., 1985).

The peptides of the invention can also be administered via liposomes,which serve to target the peptides to a particular tissue, such aslymphoid tissue, or to target selectively to infected cells, as well asto increase the half-life of the peptide composition. Liposomes includeemulsions, foams, micelles, insoluble monolayers, liquid crystals,phospholipid dispersions, lamellar layers and the like. In thesepreparations, the peptide to be delivered is incorporated as part of aliposome, alone or in conjunction with a molecule which binds to areceptor prevalent among lymphoid cells (such as monoclonal antibodieswhich bind to the CD45 antigen) or with other therapeutic or immunogeniccompositions. Thus, liposomes either filled or decorated with a desiredpeptide of the invention can be directed to the site of lymphoid cells,where the liposomes then deliver the peptide compositions. Liposomes foruse in accordance with the invention are formed from standardvesicle-forming lipids, which generally include neutral and negativelycharged phospholipids and a sterol, such as cholesterol. The selectionof lipids is generally guided by consideration of, e.g., liposome size,acid lability and stability of the liposomes in the blood stream. Avariety of methods are available for preparing liposomes, as describedin, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), andU.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

For targeting compositions of the invention to cells of the immunesystem, a ligand can be incorporated into the liposome, e.g., antibodiesor fragments thereof specific for cell surface determinants of thedesired immune system cells. A liposome suspension containing a peptidemay be administered intravenously, locally, topically, etc. in a dosewhich varies according to, inter alia, the manner of administration, thepeptide being delivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be usedwhich include, for example, pharmaceutical grades of mannitol, lactose,starch, magnesium stearate, sodium saccharin, talcum, cellulose,glucose, sucrose, magnesium carbonate, and the like. For oraladministration, a pharmaceutically acceptable nontoxic composition isformed by incorporating any of the normally employed excipients, such asthose carriers previously listed, and generally 10-95% of activeingredient, that is, one or more peptides of the invention, often at aconcentration of 25%-75%.

For aerosol administration, the immunogenic peptides are preferablysupplied in finely divided form, along with a surfactant and propellant.Typical percentages of peptides are 0.01%-20% by weight, often 1%-10%.The surfactant must, of course, be pharmaceutically acceptable, andpreferably soluble in the propellant. Representative of such agents arethe esters or partial esters of fatty acids containing from 6 to 22carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic,linoleic, linolenic, olesteric and oleic acids with an aliphaticpolyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixedor natural glycerides may be employed. The surfactant may constitute0.1%-20% by weight of the composition, preferably 0.25-5%. The balanceof the composition is ordinarily propellant, although an atomizer may beused in which no propellant is necessary and other percentages areadjusted accordingly. A carrier can also be included, e.g., lecithin forintranasal delivery.

Antigenic peptides of the invention have been used to elicit a CTLand/or

HTL response ex vivo, as well. The resulting CTLs or HTLs can be used totreat chronic infections, or tumors in patients that do not respond toother conventional forms of therapy, or who do not respond to atherapeutic peptide or nucleic acid vaccine in accordance with theinvention. Ex vivo CTL or HTL responses to a particular antigen(infectious or tumor-associated) are induced by incubating in tissueculture the patient's, or genetically compatible, CTL or HTL precursorcells together with a source of antigen-presenting cells (APC), such asdendritic cells, and the appropriate immunogenic peptide. After anappropriate incubation time (typically about 7-28 days), in which theprecursor cells are activated and expanded into effector cells, thecells are infused back into the patient, where they will destroy (CTL)or facilitate destruction (HTL) of their specific target cell (aninfected cell or a tumor cell).

Kits

The peptide and nucleic acid compositions of this invention can beprovided in kit form together with instructions for vaccineadministration. Typically the kit would include desired composition(s)of the invention in a container, preferably in unit dosage form andinstructions for administration. For example, a kit would include anAPC, such as a dendritic cell, previously exposed to and now presentingpeptides of the invention in a container, preferably in unit dosage formtogether with instructions for administration. An alternative kit wouldinclude a minigene construct with desired nucleic acids of the inventionin a container, preferably in unit dosage form together withinstructions for administration. Lymphokines such as IL-2 or IL-12 mayalso be included in the kit. Other kit components that may also bedesirable include, for example, a sterile syringe, booster dosages, andother desired excipients.

The invention will be described in greater detail by way of specificexamples. The following examples are offered for illustrative purposes,and are not intended to limit the invention in any manner. Those ofskill in the art will readily recognize a variety of non-criticalparameters that can be changed or modified to yield alternativeembodiments in accordance with the invention.

EXAMPLES Example 1 Selection of Tumor Associated Antigens

Because the A2 supertype is broadly expressed in the population(39-49%), peptides which bind to this family of molecules provide areasonable basis for peptide-based vaccines. While the A2 vaccinetargets patients that express HLA-A2 molecules, the approach can bereadily extended to include peptide(s) that bind to additional allelesor supertype groups thereof (see, e.g., U.S. Provisional Application No.60/432,017, filed 10 Dec. 2002; which is herein incorporated byreference in its entirety).

Whole proteins often induce an immune response limited to specificepitopes that may be ineffective in mediating effective anti-tumorimmune responses (Disis et al., J. Immunology 156:3151-3158 (1996);Manca et al., J. Immunology 146:1964-1971 (1991)). An epitope-basedvaccine circumvents this limitation through the identification ofpeptide epitopes embedded in TAAs. Exemplary TAAs are set forth in Table3.

Peptides were evaluated based upon MHC binding motifs, on the capacityto bind MHC molecules, and the ability to activate tumor-reactive CTL invitro using lymphocyte cultures from normal individuals. This approachhas several advantages. First, it does not require the isolation ofpatient-derived cells such as CTL or tumor cells. Secondly, theidentification of epitopes that stimulate CTL in normal individualspermits the identification of a broad range of epitopes, includingsubdominant as well as dominant epitopes.

Four tumor-associated antigens, CEA, p53, MAGE 2/3 and HER2/neu, areexpressed in various tumor types (Kawashima et al., Human Immunology59:1-14 (1998); Tomlinson, et al., Advanced Drug Delivery Reviews, Vol.32(3) (6 Jul. 1998)). In a preferred embodiment, a vaccine comprisesepitopes (as one or more peptides or as nucleic acids encoding them)from among these four, or any other, TAAs. Accordingly, this vaccineinduces CTL responses against several major cancer types.

Carcinoembryonic antigen is a 180 kD mw cell surface and secretedglycoprotein overexpressed on most human adenocarcinomas. These includecolon, rectal, pancreatic and gastric (Muraro, 1985) as well as 50% ofbreast (Steward, 1974) and 70% of non-small cell lung carcinomas(Vincent, 1978). This antigen is also expressed on normal epithelium andin some fetal tissue (Thompson, 1991).

The HER2/neu antigen (185 kDa) is a transmembrane glycoprotein withtyrosine kinase activity whose structure is similar to the epidermalgrowth factor receptor (Coussens, 1985; Bargmann, 1986; Yamamoto, 1986).Amplification of the HER2/neu gene and/or overexpression of theassociated protein have been reported in many human adenocarcinomas ofthe breast (Slamon, 1987 and 1989; Borg, 1990), ovary (Slamon, 1989),uterus (Berchuck, 1991; Lukes, 1994), prostate (Kuhn, 1993; Sadasivan,1993), stomach (Yonemura, 1991; Kameda, 1990; Houldsworth, 1990),esophagus (Houldsworth, 1990), pancreas (Yamanaka, 1993), kidney(Weidner, 1990) and lung (Kern, 1990; Rachwal, 1995).

The MAGE, melanoma antigen genes, are a family of related proteins thatwere first described in 1991. Van der Bruggen and co-workers were ableto identify the MAGE gene after isolating CTLs from a patient whodemonstrated spontaneous tumor regression. These CTLs recognizedmelanoma cell lines as well as tumor lines from other patients allexpressing the same HLA-A1 restricted gene (van der Bruggen, 1991; DePlaen, 1994). The MAGE genes are expressed in metastatic melanomas(Brasseur, 1995), non-small lung (Weynants, 1994), gastric (Inoue,1995), hepatocellular (Chen, 1999), renal (Yamanaka, 1998) colorectal(Mori, 1996), and esophageal (Quillien, 1997) carcinomas as wells astumors of the head and neck (Lee, 1996), ovaries (Gillespie, 1998;Yamada, 1995), bladder (Chaux, 1998) and bone (Sudo, 1997). They arealso expressed on normal tissue, specifically placenta and male germcells (De Plaen, 1994). However, these normal cells do not express MHCClass I molecules and therefore do not present MAGE peptides on theirsurface.

In this study and previous work to identify A2 superfamily epitopes(Kawashima, 1998), MAGE-2 and MAGE-3 were considered a single TAA, basedon the expression patterns and predicted primary amino acid sequences ofthe two genes. These two members of the MAGE family appear to becoordinately regulated (Zakut, 1993), resulting in a distribution incancers that appears to be very similar, if not identical. Therefore,immune responses directed at either antigen should provide coverage fortreatment of the cancers expected to express these TAA. The MAGE-2 andMAGE-3 proteins are 84% identical at the primary amino acid level. As aresult, some epitopes are identical in the two antigens, while othersare unique to one or the other. It should be noted that two subtypes ofMAGE-2, designated “a” and b″, have been reported (Zakut, 1993). Thegene referred to herein as MAGE-2 corresponds to the MAGE-2a subtype (C.Dahlberg personal communication, NB 1056, p. 16; Van der Bruggen, 1991;Zakut, 1993).

The fourth TAA selected for use in the vaccine is p53. In normal cellsthe p53 gene induces a cell cycle arrest which allows DNA to be checkedfor irregularities and maintains DNA integrity (Kuerbitz, 1992).Mutations in the gene abolish its suppressor function and allow escapeof transformed cells from the restriction of controlled growth. At thesame time, these mutations lead to overexpression of both wildtype andmutated p53 (Levine, 1991) making it more likely that epitopes withinthe protein may be recognized by the immune system. The most commonmutations are at positions 175, 248, 273 and 282 and have been observedin colon (Rodrigues, 1990), lung (Fujino, 1995), prostate (Eastham,1995), bladder (Vet, 1995) and bone cancers (Abudu, 1999; Hung, 1997).

Table 5 below delineates the tumor antigen expression in breast, colonand lung. By targeting four TAA, the likelihood of the mutation of tumorcells (tumor escape) into cells which do not express any of the tumorantigens is decreased. Preferably, the inclusion of two or more epitopesfrom each TAA serves to increase the likelihood that individuals ofdifferent ethnicity will respond to the vaccine and provides broadenedpopulation coverage.

This rational approach to vaccine compositions can be focused on aparticular HLA allele, or extended to various HLA molecules orsupertypes to further extend population coverage.

Table 6 shows the incidence, 5-year survival rates, and the estimatednumber of deaths per year for these tumors in the U.S. for each type ofcancer in Table 5. In terms of estimated new cases, estimated deaths and5 year survival rates each of these tumor types has a large unmet need.Globally, the incidence of these tumors is significantly greater.

Example 2 A Padre® Molecule as a Helper Epitope for Enhancement of CTLInduction

There is increasing evidence that HTL activity is critical for theinduction of long lasting CTL responses (Livingston et al. J. Immunol.162:3088-3095 (1999); Walter et al., New Engl. J. Med. 333:1038-1044(1995); Hu et al., J. Exp. Med. 177:1681-1690 (1993)). Therefore, one ormore peptides that bind to HLA class II molecules and stimulate HTLs canbe used in accordance with the invention. Accordingly, a preferredembodiment of a vaccine includes a molecule from the PADRE® family ofuniversal T helper cell epitopes (HTL) that target most DR molecules ina manner designed to stimulate helper T cells. For instance, apan-DR-binding epitope peptide having the formula: aKXVAAZTLKAAa, where“X” is either cyclohexylalanine, phenylalanine, or tyrosine; “Z” iseither tryptophan, tyrosine, histidine or asparagine; and “a” is eitherD-alanine or L-alanine (SEQ ID NO:29), has been found to bind to mostHLA-DR alleles, and to stimulate the response of T helper lymphocytesfrom most individuals, regardless of their HLA type.

A particularly preferred PADRE® molecule is a synthetic peptide,aKXVAAWTLKAAa (a=D-alanine, X=cyclohexylalanine), containing non-naturalamino acid residues, specifically engineered to maximize both HLA-DRbinding capacity and induction of T cell immune responses.

Alternative preferred PADRE® molecules are the peptide's, aKFVAAWTLKAAa,aKYVAAWTLKAAa, aKFVAAYTLKAAa, aKXVAAYTLKAAa, aKYVAAYTLKAAa,aKFVAAHTLKAAa, aKXVAAHTLKAAa, aKYVAAHTLKAAa, aKFVAANTLKAAa,aKXVAANTLKAAa, aKYVAANTLKAAa, AKXVAAWTLKAAA (SEQ ID NO:30),AKFVAAWTLKAAA (SEQ ID NO:31), AKYVAAWTLKAAA (SEQ ID NO:32),AKFVAAYTLKAAA (SEQ ID NO:33), AKYVAAYTLKAAA (SEQ ID NO:34),AKYVAAYTLKAAA (SEQ ID NO:35), AKFVAAHTLKAAA (SEQ ID NO:36),AKXVAAHTLKAAA (SEQ ID NO:37), AKYVAAHTLKAAA (SEQ ID NO:38),AKFVAANTLKAAA (SEQ ID NO:39), AKXVAANTLKAAA (SEQ ID NO:40),AKYVAANTLKAAA (SEQ ID NO:41) (a=D-alanine, X=cyclohexylalanine).

In a presently preferred embodiment, the PADRE® peptide is amidated. Forexample, a particularly preferred amidated embodiment of a PADRE®molecule is conventionally written aKXVAAWTLKAAa-NH₂.

Competitive inhibition assays with purified HLA-DR moleculesdemonstrated that the PADRE® molecule aKXVAAWTLKAAa-NH₂ binds with highor intermediate affinity (IC₅₀≦1,000 nM) to 15 out of 16 of the mostprevalent HLA-DR molecules ((Kawashima et al., Human Immunology 59:1-14(1998); Alexander et al., Immunity 1:751-761 (1994)). A comparison ofthe DR binding capacity of PADRE® and tetanus toxoid (TT) peptide830-843, a “universal” epitope has been published (Panina-Bordignon etal., Eur. J. Immunology 19:2237-2242 (1989)). The TT 830-843 peptidebound to only seven of 16 DR molecules tested, while PADRE® bound 15 of16. At least 1 of the 15 DR molecules that bind PADRE® is predicted tobe present in >95% of all humans. Therefore, this PADRE® molecule isanticipated to induce an HTL response in virtually all patients, despitethe extensive polymorphism of HLA-DR molecules in the human population.

Early data from a phase I/II investigator-sponsored trial, conducted atthe University of Leiden (C. J. M. Melief), support the principle thatthe PADRE® molecule aKXVAAWTLKAAa, possibly the amidated aKXVAAWTLKAAa-NH₂, is highly immunogenic in humans (Ressing et al., J. Immunother.23(2):255-66 (2000)). In this trial, a PADRE® molecule was co-emulsifiedwith various human papilloma virus (HPV)-derived CTL epitopes and wasinjected into patients with recurrent or residual cervical carcinoma.However, because of the late stage of carcinoma with the study patients,it was expected that these patients were immunocompromised. Thepatients' immunocompromised status was demonstrated by their lowfrequency of influenza virus-specific CTL, reduced levels of CD3expression, and low incidence of proliferative recall responses after invitro stimulation with conventional antigens. Thus, no efficacy wasanticipated in the University of Leiden trial, rather the goal of thattrial was essentially to evaluate safety. Safety was, in fact,demonstrated.

Thus, the PADRE® peptide component(s) of the vaccine bind with broadspecificity to multiple allelic forms of HLA-DR molecules. Moreover,PADRE® peptide component(s) bind with high affinity (IC₅₀≦1000 nM),i.e., at a level of affinity correlated with being immunogenic for HLAClass II restricted T cells. The in vivo administration of PADRE®peptide(s) stimulates the proliferation of HTL in normal humans as wellas patient populations.

One or more PADRE® peptide(s) may be included in a composition, e.g., avaccine, comprising one or more peptides, either as an individualpeptide(s), fused to one or more CTL peptides (epitope and/or analog),or both.

Example 3 Functional Competence of ProGP-Derived DC

One embodiment of a vaccine in accordance with the invention comprisesepitope-bearing peptides of the invention delivered via dendritic cells(DC). Accordingly, DC were evaluated in both in vitro and in vivo immunefunction assays. These assays include the stimulation of CTL hybridomasand CTL cell lines, and the in vivo activation of CTL.

DC Purification

ProGP-mobilized DC were purified from peripheral blood (PB) and spleensof ProGP-treated C57B1/6 mice to evaluate their ability to presentantigen and to elicit cellular immune responses. Briefly, DC werepurified from total WBC and spleen using a positive selection strategyemploying magnetic beads coated with a CD11c specific antibody (MiltenyiBibtec, Auburn Calif.). For comparison, ex vivo expanded DC weregenerated by culturing bone marrow cells from untreated C57B1/6 micewith the standard cocktail of GM-CSF and IL-4 (R&D Systems, Minneapolis,Minn.) for a period of 7-8 days (Mayordomo et al., Nature Med.1:1297-1302 (1995)). Recent studies have revealed that this ex vivoexpanded DC population contains effective antigen presenting cells, withthe capacity to stimulate anti-tumor immune responses (Celluzzi et al.,J. Exp. Med. 83:283-287 (1996)).

The purities of ProGP-derived DC (100 μg/day, 10 days, SC) andGM-CSF/IL-4 ex vivo expanded DC were determined by flow cytometry. DCpopulations were defined as cells expressing both CD11c and MHC Class IImolecules. Following purification of DC from magnetic CD11c microbeads,the percentage of double positive PB-derived DC, isolated fromProGP-treated mice, was enriched from approximately 4% to a range from48-57% (average yield=4.5×10⁶ DC/animal) The percentage of purifiedsplenic DC isolated from ProGP treated mice was enriched from a range of12-17% to a range of 67-77%. The purity of GM-CSF/IL-4 ex vivo expandedDC ranged from 31-41% (Wong et al., J. Immunother., 21:32040 (1998)).

In Vitro Stimulation of CTL Hybridomas and CTL Cell Lines: Presentationof Specific CTL Epitopes

The ability of ProGP generated DC to stimulate a CTL cell line wasdemonstrated in vitro using a viral-derived epitope and a correspondingepitope responsive CTL cell line. Transgenic mice expressing humanHLA-A2.1 were treated with ProGP. Splenic DC isolated from these micewere pulsed with a peptide epitope derived from hepatitis B virus (HBVPol 455) and then incubated with a CTL cell line that responds to theHBV Pol 455 epitope/HLA-A2.1 complex by producing IFNγ. The capacity ofProGP-derived splenic DC to present the HBV Pol 455 epitope was greaterthan that of two positive control populations: GM-CSF and IL-4 expandedDC cultures, or purified splenic B cells (FIG. 3B). The left shift inthe response curve for ProGP-derived spleen cells versus the otherantigen presenting cells reveal that these ProGP-derived cells requireless epitope to stimulate maximal IFNγ release by the responder cellline.

Example 4 Peptide-Pulsed ProGP-Derived Dc Promote In Vivo CTL Responses

The ability of ex vivo peptide-pulsed DC to stimulate CTL responses invivo was also evaluated using the HLA-A2.1 transgenic mouse model. DCderived from ProGP-treated animals or control DC derived from bonemarrow cells after expansion with GM-CSF and IL-4 were pulsed ex vivowith the HBV Pol 455 CTL epitope, washed and injected (IV) into suchmice. At seven days post immunization, spleens were removed andsplenocytes containing DC and CTL were restimulated twice in vitro inthe presence of the HBV Pol 455 peptide. The CTL activity of threeindependent cultures of restimulated spleen cell cultures was assessedby measuring the ability of the CTL to lyse ⁵¹Cr-labeled target cellspulsed with or without peptide. Vigorous CTL responses were generated inanimals immunized with the epitope-pulsed ProGP derived DC as well asepitope-pulsed GM-CSF/IL-4 DC (FIG. 4). In contrast, animals that wereimmunized with mock-pulsed ProGP-generated DC (no peptide) exhibited noevidence of CTL induction. These data confirm that DC derived from ProGPtreated mice can be pulsed ex vivo with epitope and used to inducespecific CTL responses in vivo. Thus, these data support the principlethat ProGP-derived DC promote CTL responses in a model that manifestshuman MHC Class I molecules.

In vivo pharmacology studies in mice have demonstrated no apparenttoxicity of reinfusion of pulsed autologous DC into animals.

Example 5 Dendritic Cell Isolation, Pulsing, Testing and Administration

A presently preferred procedure for vaccination is set forth herein. Inbrief, patients are treated with ProGP to expand and mobilize DC intothe circulation. On the day of peak DC mobilization, determined inaccordance with procedures known in the art, patients undergoleukapheresis (approximately 15 L process, possibly repeated once ifrequired to collect sufficient mononuclear cells). The mononuclear cellproduct is admixed with peptides of the invention by injection throughmicropore filters (this admixing protocol is not needed if sterilepeptides are used). After incubation and washing to remove residualunbound peptides, the cell product vaccine embodiment is resuspended incryopreservative solution (final 10% DMSO) and, for those protocolsinvolving multiple vaccination boosts, divided into aliquots. The pulsedmononuclear cell product(s) are frozen and stored according to acceptedprocedures for hematopoietic stem cells.

Vaccination is performed by injection or intravenous infusion of thawedcell product after the hematologic effects of ProGP in the patient havedissipated (i.e., the hemogram has returned to baseline). FIG. 5provides a flow chart of ex vivo pulsing of DC with peptides, washing ofDC, DC testing, and cryopreservation. A more detailed description of theprocess is provided in the following Examples.

Example 6 Administration of ProGP and Collection of Mononuclear Cells byLeukapheresis

Patients are treated with ProGP daily by subcutaneous injection (doseand schedule determined in accordance with standard medical procedures).On the evening before leukapheresis, patients are assessed by anapheresis physician or nurse/technologist for adequacy of intravenousaccess for large-bore apheresis catheters. If peripheral venous accessis deemed inadequate to maintain rapid blood flow for apheresis, thencentral venous catheters (inguinal, subclavian or internal jugularsites) can be inserted by appropriate medical/surgical personnel. On theday of predicted peak DC mobilization, leukapheresis (approximately 3blood volumes or 15 L) is performed, for example, on a Cobe Spectra orFenwal CS3000 (flow rate≧35 mL/min) to obtain mononuclear cells. Thenumber of DC in the leukapheresis product is estimated by flowcytometric counting of mononuclear cells possessing the immunophenotypeslin-/HLA-DR+/CD11c+ and lin-/HLA-DR+/CD123+ in a 1 mL sample asepticallywithdrawn from the apheresis product. The numbers of granulocytes andlymphocytes in the leukapheresis product are counted by automatedcytometry (CBC/differential). CBC/differential is performed immediatelyafter the leukapheresis procedure and every other day for ten days tomonitor resolution of the hematologic effects of the hematopoietintreatment and apheresis.

Example 7 A Procedure for Dendritic Cell Pulsing

Plasma is removed from the leukapheresis product by centrifugation andexpression of supernatant. The cells from the centrifugation pellet areresuspended in OptiMEM medium with 1% Human Serum Albumin (HSA) at acell density of 10⁷ DC/ml in up to 100 ml.

The peptide(s) of the invention, preferably as individual sterile A2peptide formulations, are administered directly into the DC culture bagthrough an injection port, using aseptic technique. After mixing, e.g.,by repeated squeezing and inversion, the cell suspension is incubatedfor four hours at ambient temperature. Cryopreservative solution isprepared by dissolving 50 mL pharmaceutical grade dimethylsulfoxide(DMSO) in 200 mL Plasmalyte®. After the pulsing period, the cellsuspension is washed by centrifugation and resuspension in an equalvolume of phosphate buffered saline solution. The washing procedure isrepeated a defined number of times, e.g., until studies validate thatpeptides have been removed. Samples of one milliliter each are removedfor viability testing and microbiological testing. The cells are thenprepared for freezing by centrifugation and resuspension in an equalvolume of cryopreservative solution (final 10% DMSO). The cellsuspension in cryopreservative is then divided into six equal aliquots,transferred to 50 ml freezing bags (Fenwal) and frozen at controlledrate of PC/min for storage in liquid nitrogen until needed forvaccination procedure.

Assay to Evaluate the Pulsing Procedure

Antigen presenting cells, long-term stimulated T cells corresponding topeptides of the invention, or T cell hybridomas, are used to determinethe optimal procedure for incubating the peptide reagents of a vaccinewith human cells. Pulsing studies are done using one or more of thefollowing cell sources: purified DC from ProGP treated HLA-A2.1transgenic mice; human tumor cell lines that express HLA-A2; peripheralblood mononuclear cells from normal human volunteers; peripheral bloodmononuclear cells from ProGP treated patients; and/or DC obtained fromnormal human HLA-A2 Volunteers following the ex vivo culture of theirperipheral blood mononuclear cells with GM-CSF and IL-4.

Evaluated conditions include, e.g.:

-   -   Cellular isolation procedure and cell number    -   Concentration of vaccine peptides    -   Washing conditions to remove ancillary reagents    -   Post-pulsing manipulations (resuspension, freezing)

Accordingly, these studies demonstrate the ability of the procedure toproduce functional HLA-A2/peptide complexes on the surface of the humancells. The validation of the pulsing procedure is established usingHLA-A2.1-specific T cell lines after which the Phase I clinical trialoccurs.

Example 8 Validation of Peptide Removal from the DC Product

Following pulsing with the peptide reagents, DC from the patient arewashed several times to remove excess peptides prior to infusing thecells back into the patient. In this embodiment of a vaccine of theinvention, the washing procedure removes unbound peptides. Accordingly,there is no, or negligible, systemic, exposure of the patient to thepeptides. Alternative vaccines of the invention involve directadministration of peptides of the invention to a patient, administrationof a multiepitopic polypeptide comprising one or more peptides of theinvention, administration of the peptides in a form of nucleic acidswhich encode them, e.g., by use of minigene constructs, or by viralvectors.

Assay for Vaccine Peptides in the Dendritic Cell Wash Buffer

After the DC are incubated with the peptides, the cells are washed withmultiple volumes of wash buffer. An aliquot of the last wash is placedonto a nonpolar solid-phase extraction cartridge and washed to reducethe salt content of the sample. Any peptides contained in the bufferwill be eluted from the extraction cartridge and evaporated to dryness.The sample is then reconstituted in High Performance LiquidChromatography (HPLC) mobile phase, injected onto a polymer basedreverse-phase HPLC column, and eluted using reverse-phase gradientelution chromatography. Residual peptides are detected using a massspectrometer set-up to monitor the protonated molecular ions of eachpeptide as they elute from the HPLC column. The peptides are quantifiedby comparing the area response ratio of analyte and internal standard tothat obtained for standards in a calibration curve.

Example 9 Validation of Trifluoroacetic Acid Removal from the DC Product

In a particular embodiment, peptide reagents may be formulated using0.1% trifluoroacetic acid (TFA). The washing procedure developed toremove residual peptide also removes residual TFA.

Example 10 Dendritic Cell Release Testing Identity

The number of DC in the leukapheresis product is estimated by flowcytometric counting of mononuclear cells possessing the immunophenotypeslin⁻/HLA-DR⁺/CD11c⁺ and lin⁻/HLA-DR⁺/CD123⁺ in a 1 ml sample asepticallywithdrawn from the apheresis product. Lin⁻ cells excludes monocytes,T-lymphocytes, B-lymphocytes, and granulocytes, by using a cocktail ofantibodies to lineage markers CD3, CD14, DC16, CD19, CD20, CD56.

Cell Viability

Viability of mononuclear cells is assessed after pulsing and washing,prior to suspension in cryopreservative, by trypan blue dye exclusion.In general, if the cell product contains more than 50% trypanblue-positive cells, the product is not administered to a patient.

Microbiological Testing

The cell suspension in cryopreservative is examined for microbialcontamination by gram stain and routine clinical bacterial and fungalculture/sensitivity. If tests are positive for bacterial or fungalcontamination, implicit evidence of significant contamination, theproduct is not infused. If, e.g., a gram stain is negative, the productmay be infused for the first vaccination while awaiting results ofculture/sensitivity. Antibiotic therapy based on culture results isinstituted at the discretion of the treating physician if the patientshows appropriate signs of infection that could be clinicallyattributable to the infused contaminant.

Example 11 Patient Vaccination

In a preferred embodiment, an aliquot of frozen pulsed dendritic cellproduct is removed from a liquid nitrogen freezer and kept frozen in aninsulated vessel containing liquid nitrogen during transport to theinfusion site. The product is thawed by immersion with gentle agitationin a water bath at 37° C. Immediately on thawing, the cell suspension isinfused through intravenous line by gravity or by syringe pump.Alternatively, the vaccine is administered by injection, e.g.,subcutaneously, intradermally, or intramuscularly. The patient's vitalsigns are monitored before infusion/injection and at 5 minute intervalsduring an infusion, then at 15 minute intervals for 1 hour afterinfusion/injection.

Infusion protocols in accordance with knowledge in the art are carriedout for alternative vaccine embodiments of the invention, such as directpeptide infusion or nucleic acid administration.

Example 12 Identification of A2 Supermotif/Motif-Bearing Peptides

Nine CTL epitopes derived from well-characterized tumor antigens(MAGE-2/3, HER-2/neu, p53, and CEA) were selected for the currentvaccine using a 3-step process: 1) computer motif analysis of theprimary protein sequence to identify motif-containing peptides that willthus have a high likelihood of binding HLA-A2 supertype molecules; 2)direct measurement of MHC binding affinity of the motif-containingpeptides to A2 supertype alleles; and 3) immunogenicity testing ofhigh-affinity MHC binding peptides for CTL induction. In addition toidentifying native-sequence epitopes, modified epitope analogs weredesigned to provide enhanced immunogenicity. Analogs were generated bysubstituting key amino acid residues that enhance either MHC bindingaffinity or T Cell Receptor (TCR) interaction.

The final vaccine product, EP-2101, is a pool of the ninetumor-associated CTL epitopes (natural and analog sequences) and aPADRE® universal epitope, administered to cancer patients as an emulsionin Montanide® ISA 51 adjuvant. The vaccine is similar to syntheticpeptide vaccines (containing one or more peptides) that have been testedby other investigators in cancer patients where CTL induction, positiveclinical responses, and vaccine safety have been described (Cormier, J.N., et al., Cancer J. Sci. Am. 3:37-44 (1997); Salgaller, M. L., et al.,Cancer Res. 56:4749-4757 (1996); Wang, F., et al., Clin. Cancer Res.5:2756-2765 (1999); Muderspach, L., et al., Clin. Cancer Res.6:3406-3416 (2000); Ressing, M. E., et al., J Immunother. 23:255-266(2000)). All of the EP-2101 epitopes are immunogenic, using peripheralblood mononuclear cells (PBMC) from HLA-A2.1 positive subjects and an invitro primary induction assay, in inducing CTLs that respond to thepeptide and to tumor cell lines that express the TAA and present thewild-type epitope (Keogh, E., et al., J. Immunol. 167:787-796 (2001);Kawashima, I., et al., Hum. Immunol. 59:1-14 (1998)). The epitopes werealso shown to be immunogenic when tested in an HLA-A2.1/K^(b) transgenicmouse model used to determine the immunogenicity of HLA-A2.1-restrictedhuman epitopes (Wentworth, P. A., et al., Eur. J. Immunol. 26:97-101(1996); Vitiello, A., et al., J Exp. Med. 173:1007-1015 (1991);Lustgarten, J., et al., Hum. Immunol. 52:109-118 (1997)).

Native Epitope Sequences

A computer-based motif and algorithm search was performed on the primaryamino acid sequences of CEA, MAGE-2/3, HER-2/neu, and p53 to predictpeptides most likely to bind the MHC molecules of the five alleles ofthe HLA-A2 supertype family (Tables 4D and 6) (Sette, A. and J. Sidney,Immunogenetics 50:201-212 (1999)). Motif and algorithm-positive peptideswere then synthesized and tested for binding to purified HLA-A2.1, themolecule most frequently expressed in humans as well as other MHCmolecules of the HLA-A2 supertype family.

In the final step of the epitope screening process, peptides with highcross-reactive MHC binding to the HLA-A2 supertype family receptors weretested for immunogenicity. The assay is an in vitro primary CTLinduction system where CD8⁺ PBMC from normal subjects are stimulated invitro, initially with peptide-loaded dendritic cells (DCs) (adherentPBMC expanded in GM-CSF and IL-4), followed by two weekly cycles ofrestimulation with peptide (Keogh, E., et al., J. Immunol. 167:787-796(2001); Kawashima, I., et al., Hum. Immunol. 59:1-14 (1998)). Followingexpansion of naïve precursor cells, CTL activity is determined in thepresence of HLA-A2.1 positive target cells and wild-type peptide, usingcytotoxicity (⁵¹Cr-release assay) or interferon-gamma (IFN-γ)production(ELISA) as the read-out. Immunogenic peptides that induced CTL werefurther tested for responses against the naturally processed epitopeexpressed on tumor cell lines. Epitopes that induced tumor-reactive CTLwere considered as vaccine candidates.

Fixed Anchor Analogs

To break tolerance and improve CTL induction against weakly immunogenicepitopes, tumor-associated peptides with low MHC binding activity weremodified to enhance their binding by substituting suboptimalMHC-interacting anchor residues with optimal, motif-associated residues(Kawashima, I., et al., Hum. Immunol. 59:1-14 (1998); Parkhurst, M. R.,et al., J Immunol. 157:2539-2548 (1996)). This strategy of “fixing”anchor residues has been described for a number of tumor and infectiousdisease epitopes and these analogs have demonstrated enhanced in vivoimmunogenicity compared to the wild-type epitope (Kawashima, I., et al.,Hum. Immunol. 0.59:1-14 (1998); Vierboom, M. P., et al., J. Immunother.21:399-408 (1998)), a finding that is correlated with increased MECbinding (Parkhurst, M. R, et J. Immunol. 157:2539-2548 (1996)). Thedisease relevance of fixed-anchor analogs has been demonstrated by theircapacity to induce not only stronger CTL responses, but also CTL thatcross-react against the native wild-type epitope expressed on tumorcells (Kawashima, I., et al., Hum. Immunol. 59:1-14 (1998); Vierboom, M.P., et al., J Immunother. 21:399-408 (1998); Sarobe, P., et al., J.Clin. Invest 102:1239-1248 (1998)). More importantly, significant tumorregression has been observed in melanoma patients immunized with afixed-anchor epitope in conjunction with IL-2 therapy (Rosenberg, S. A.,et al., Nat. Med. 4:321-327 (1998)).

Heteroclitic Analogs

A second strategy was also used to generate analogs with improvedpotency for CTL induction. Amino acid substitutions that affect TCRcontact residue(s) were introduced into known CTL epitopes, since theseanalogs have been shown to induce stronger responses than the wild-typeepitope (Zaremba, S., et al., Cancer Res. 57:4570-4577 (1997); Zugel,U., R. et al., J. Immunol. 161:1705-1709 (1998); Rivoltini, L., P., etal., Cancer Res. 59:301-306 (1999); Slansky, J. E., et al., Immunity.13:529-538 (2000)). The T cell response stimulated by heterocliticanalogs compared to the wild-type epitope is manifested both as anincrease in the response magnitude as well as an enhancement in TCRavidity (Zugel, U., R. et al., J Immunol. 161:1705-1709 (1998);Rivoltini, L., P., et al., Cancer Res. 59:301-306 (1999); Slansky, J.E., et al., Immunity. 13:529-538 (2000); Tangri, S., et al., J. Exp.Med. 194:833-846 (2001)), with the latter thought to be a potentialmechanism for heteroclicity (Slansky, J. E., et al., Immunity.13:529-538 (2000)).

Heteroclitic analogs are potentially important in cancer vaccines notonly for their ability to induce strong T cell responses, but also fortheir ability to break T cell tolerance. These properties have beendemonstrated in animal as well as human trials (Zugel, U., R. et al., J.Immunol. 161:17054709 (1998); Slansky, J. E., et al., Immunity.13:529-538 (2000); Fong, L., et al., Proc. Natl. Acad. Sci. U.S.A98:8809-8814 (2001)). In humans, significant anti-tumor responses wererecently reported in a trial examining treatment of colon cancer andNSCLC patients with DCs loaded with a heteroclitic analog of a CEAepitope, referred to as CAP1-6D (designated herein as CEA.605D6, peptide1350.01), that was initially described by Zaremba et al. (Zaremba, S.,et al., Cancer Res. 57:4570-4577 (1997)). In this clinical study (Fong,L., et al., Proc. Natl. Acad. Sci. U.S.A 98:8809-8814 (2001)), fiveclinical responders were observed out of 12 patients who received the DCvaccine, and a correlation was observed between clinical response and anincrease in the percentage of analog-specific CD8⁺ T cells followingvaccination as detected by tetramer staining. During our preclinicalstudies, heteroclitic analogs were identified which led to thegeneration of six new analogs modified from three known tumor epitopes,MAGE-3.112, MAGE-2.157, and CEA.691 (Tangri, S., et al., J. Exp. Med.194:833-846 (2001)). All of these analogs induce strong primary humanCTL responses in vitro that cross-react against the native epitopeexpressed by tumor cells (Tangri, S., et al., J Exp. Med. 194:833-846(2001)).

Using the epitope selection process described above, nine epitopes wereselected for the vaccine product. These epitopes, shown in Tables 3 and7, were chosen on the basis of demonstrating 1) broad tumor antigencoverage with a mix of CTL native sequence epitopes, fixed-anchoranalogs and heteroblitic analogs; 2) high cross-reactive bindingaffinity for HLA-A2 supertype alleles; 3) immunogenicity in the in vitrohuman primary CTL induction assay, particularly in generating CTL thatrespond to wild-type, epitope-expressing tumor cells; and, 4) whereveravailable, published reports in the literature showing primary orpost-vaccination CTL responses in normal subjects or cancer patients.

Pursuant to our clinical objective of inducing a broad multi-epitope,multi-antigen response in cancer patients, two epitopes are representedfrom each of three TAAs (HER-2/neu, p53, and MAGE-2/3) and threeepitopes from CEA, a more widely expressed TAA on lung- andcolon-associated tumors. The extent of cross-reactive binding againstmultiple HLA-A2 supertype alleles should enable the vaccine to cover abroad and non-ethnically biased population among individuals expressingHLA-A2 supertype alleles.

Four of the epitopes selected are fixed-anchor analogs that weremodified for improved MHC binding. One fixed-anchor analog was derivedfrom the well-characterized HER-2/neu.369 epitope, which has been shownto induce strong recall and post-vaccination CTL responses in cancerpatients (Zaks, T. Z. and Rosenberg, S. A., Cancer Res. 58:4902-4908(1998); Knutson, K. L., et al., J. Clin. Invest 107:477-484 (2001)). Byincreasing supertype binding through substitution of both MHC anchorresidues, the V2V9 analog of HER-2/neu.369 is expected to demonstrateeven broader immunogenicity in HLA-A2 supertype individuals. Theremaining fixed-anchor analogs (CEA.24V9, p53.139L2B3, and p53.149M2)were designed from epitopes identified in the selection process and theyhave not been tested previously in the clinic. The p53.139L2B3 analogcontains an additional α-aminoisobutyric acid substitution at. 3 (anon-anchor position) to circumvent potential stability issues with thecysteine residue found in the wild-type epitope. As with the epitopesderived from wild-type sequences, all of the fixed-anchor analogs induceCTL that cross-react with the wild-type epitope presented by tumor celllines (Table 7) (Keogh, E., et al., J Immunol. 167:787-796 (2001)).

Another class of analogs represented in the current vaccine are thosewith heteroclitic activity resulting from substitution of TCR contactresidues (Zaremba, S., et al., Cancer Res. 57:4570-4577 (1997); Zugei,U., R. et al., J. Immunol. 161:1705-1709 (1998); Rivoltini, L., P., etal., Cancer Res. 59:301-306 (1999); Slansky, J. E., et al., Immunity.13:529-538 (2000)). Of the three heteroclitic analogs included, twoanalogs (MAGE-3.11215 and CEA.691H5) induce strong CTL activity whichexceeds that of the wild-type peptide (Tangri, S., et al., J. Exp. Med.194:833-846 (2001)). The third heteroclitic analog, CEA.605D6 (CAP1-6D)(Zaremba, S., et al., Cancer Res. 57:4570-4577 (1997)), is included inthe current vaccine to provide additional epitope breadth and anti-tumorCTL induction, particularly in light of recent clinical data reportingsignificant CTL and clinical responses in colon and lung cancer patientsvaccinated with DC loaded with this heteroclitic CEA analog (Fong, L.,et al., Proc. Natl. Acad. Sci. U.S.A 98:8809-8814 (2001)).

The immunogenicity of the vaccine epitopes has been corroborated,particularly in human systems, by additional reports. For example, theHER-2/neu.369 and p53.149 epitopes (wild-type versions of analogs usedin EP-2101), and HER-2/neu.689 have induced specific CTL responses usingPBMC obtained from healthy donors through primary in vitro induction(zum Buschenfelde, C. M., et al., J. Immunol. 165:4133-4140 (2000);Chikamatsu, K., et al., Clin. Cancer Res. 5:1281-1288 (1999)) as well asrecall responses using PBMC from cancer patients (Knutson, K. L., etal., J. Clin. Invest 107:477-484 (2001); Rongcun, Y., et al., J.Immunol. 163:1037-1044 (1999)). In addition, the p53.139L2, p53.149M2,HER-2/neu.369, and MAGE-2.157 epitopes were shown by others to inducepeptide and tumor cell-reactive CTL in vivo in HLA-A2.1 transgenic mice(Lustgarten, J., et al., Hum. Immunol. 0.52:109-118 (1997); Visseren, M.J., et al., Int J Cancer 73:125-130 (1997); Petersen, T. R., et al.,Scand. J. Immunol. 53:357-364 (2001); Theobald, M., et al., Proc. Natl.Acad. Sci. U.S.A 92:11993-11997 (1995)).

The final epitope included in the vaccine is a universal PADRE® epitope(Alexander, J., et al., Immunity. 1:751-761 (1994)). The PADRE® epitopewas designed to bind in a cross-reactive manner to the majority of theDR supertype alleles (Alexander, J., et al., Immunity. 1:751-761 (1994))such that >90% of the general population is predicted to respond againstthis epitope. In the current vaccine, the PADRE® epitope is included toenhance CTL induction by the pool of CTL epitopes. A number of publishedstudies have demonstrated the ability of HTL responses to augment andsupport the maintenance of CTL responses in vivo (Knutson, K. L., etal., J. Clin. Invest 107:477-484 (2001); Kalams, S. A. and Walker, B.D., J Exp. Med. 188:2199-2204 (1998); Weber, J. S, and Mule, J. J., J.Clin. Invest 107:553-554 (2001); Toes, R. E., et al., J Exp. Med.189:753-756 (1999)). Indeed, the PADRE® epitope (Muderspach, L., et al.,Clin. Cancer Res. 6:3406-3416 (2000); Ressing, M. E., et al., J.Immunother. 23:255-266 (2000); Weber, J. S., et al., J. Immunother.22:431-440 (1999)), as well as other HTL-inducing antigens and epitopes(Vitiello, A., et al., J. Clin. Invest 95:341-349 (1995); Dhodapkar, M.V., et al., J. Clin. Invest 104:173-180 (1999)), have been an integralcomponent of several clinical trial vaccines.

In summary, nine CTL epitopes representing a combination of fixed anchornative sequences and heteroclitic analogs, and one PADRE® universal HTLepitope, have been selected for inclusion of EP-2101. This set ofepitopes constitutes a unique combination of vaccine constituentsintended to provide broad antigen and population coverage among HLA-A2individuals. The CTL epitopes selected for the current vaccine arecapable of inducing CTL from naïve precursors in PBMC from normalsubjects and in cancer patients. This observation strongly suggests theabsence of complete tolerance against these tumor-associated epitopesand supports their utility for inducing beneficial CTL responses incancer patients.

Example 13 Immunogenicity of the Vaccine Epitopes and Vaccine Product

As described above, during the epitope screening process to identifyvaccine candidates, individual epitopes from TAA were tested for theircapacity to induce CTL in vitro from human PBMC obtained from HLA-A2.1individuals. All of the epitopes selected for the current vaccine wereshown to generate CTL in vitro and the CTL generated were capable ofrecognizing wild-type epitope expressed on tumor cell lines (Keogh, E.,et al., J Immunol. 167:787-796 (2001); Kawashima, I., et al., Hum.Immunol. 59:1-14 (1998); Zaremba, S., et al., Cancer Res. 57:4570-4577(1997)). These observations support the potential immunogenicity of thevaccine epitopes when administered to humans and provide furtherevidence for the existence of precursor CTL that can be primed withtumor-associated epitopes in cancer patients. The results are furthersupported by data generated from other laboratories demonstrating recallor post-vaccination CTL responses against most of the nine vaccineepitopes (including the wild-type versions of analogs in the currentvaccine) (Lustgarten, J., et al., Hum. Immunol. 52:109-118 (1997);Knutson, K. L., et al., J. Clin. Invest 107:477-484 (2001); zumBuschenfelde, C. M., et al., J. Immunol. 165:4133-4140 (2000);Chikamatsu, K., et al., Clin. Cancer Res. 5:1281-1288 (1999); Rongcun,Y., et al., J Immunol. 163:1037-1044 (1999); Visseren, M. J., et al.,Int J Cancer 73:125-130 (1997); Petersen, T. R., et al., Scand. J.Immunol. 53:357-364 (2001); Theobald, M., et al., Proc. Natl. Acad. Sci.U.S.A 92:11993-11997 (1995)).

The immunogenicity of EP-2101 was also analyzed using HLA-A2.1/K^(b)transgenic mice which express the human HLA-A2.1 molecule (see alsoExamples 15-17). These mice have been used to assess the immunogenicityof HLA-A2.1-restricted epitopes following in vivo immunization(Wentworth, P. A., et al., Eur. J. Immunol. 26:97-101 (1996); Vitiello,A., et al., J. Exp. Med. 173:1007-1015 (1991)) and while useful for invivo evaluation, they have several limitations. Our studies, using avariety of CTL epitopes, indicate that HLA transgenic mice will respondto approximately 80% of the HLA-A2.1-restricted epitopes to which humansrespond Wentworth, P. A., et al., Eur. J Immunol. 26:97-101 (1996);Wentworth, P. A., et al., Int Immunol. 8:651-659 (1996)). Also, themagnitude of the response detected for a given epitope can vary widelyfrom experiment-to-experiment, especially for responses that are lowerin magnitude. Finally, the relative magnitude of the response detectedin HLA transgenic mice will not necessarily indicate the relativemagnitude that will be induced in humans.

For the in vivo immunogenicity studies in HLA-A2.1/K^(b) transgenicmice, EP-2101 (prepared by an emulsification protocol (see Example 17)similar to that proposed for drug manufacture) was injected into miceand CTL responses against all of the epitopes in the vaccine weremeasured and compared to CTL responses induced by co-immunizing micewith each CTL epitope alone plus the PADRE® epitope, in Montanide® ISA51 adjuvant. CTL responses were determined by measuring IFN-γ productionby CTLs using an in situ ELISA (McKinney, D. M., et al.,. J. Immunol.Methods 237:105-117 (2000)), following in vitro stimulation ofsplenocytes from immunized animals with peptide. As shown in FIG. 6,based on data gathered thus far from 6-10 independent experiments, theEP-2101 vaccine appears to demonstrate immunogenicity for a majority ofCTL epitopes. For half of the CTL epitopes in EP-2101, strong CTLresponses were observed that exceeded 50 secretory units (SU) of IFN-γproduction (CEA.24V9, CEA.691H5, HER-2/neu.369V2V9, MAGE-2.157, andMAGE-3.11215). The remaining epitopes demonstrated moderate to weak CTLresponses (<10-50 SU), and these responses were generally associatedwith larger experimental variations as indicated by the larger standarddeviation bars. As discussed above, these variations reflect thelimitations of the transgenic mouse assay. However, despite the inherentvariability of the assay, the multi-epitope CTL responses induced by thepool of CTL epitopes in EP-2101 appeared comparable to CTL responsesinduced in mice by each CTL epitope alone, when co-immunized with thePADRE® epitope in Montanide® ISA 51 adjuvant. Thus, overall, theseexperiments indicate that EP-2101 is immunogenic in HLA-A2.1/K^(b)transgenic mice. Additional experiments also indicate that EP-2101 caninduce HTL responses against the PADRE® epitope in HLA-A2.1/K^(b)transgenic mice, which are restricted by the mouse H-2 I-A^(b) allele(Alexander, J., et al., Immunity. 1:751-761 (1994)).

Example 14 Immunopharmacology Study in HLA-A2.1/K^(b) Mice

EP-2101 is an immunotherapeutic vaccine designed to induce CTL responsesagainst nine peptide epitopes derived from four TAAs which are widelyexpressed on colon and lung cancer cells (CEA, p53, HER-2/neu, andMAGE-2/3). Because TAAs represent self-proteins which are over-expressedin tumor cells, induction of a therapeutic response by EP-2101 mayrequire the breaking of CTL tolerance against self-epitopes andinduction of a limited but effective CTL response, one that specificallyeliminates tumor cells without eliciting severe immunopathology againstany normal tissue that may express low levels of the same TAAs.Pre-clinical characterization of EP-2101 indicated that the vaccine isindeed immunogenic since a broad CTL response of significant magnitudewas induced in HLA-A2.1/K^(b) transgenic mice against several wild-typeand analog TAA epitopes in the vaccine (see Example 13).

The immunogenicity of the EP-2101 vaccine against multiple epitopes andmultiple self tumor proteins raised the possibility thatimmunopathological responses directed against normal tissue expressinglow levels of TAAs may be induced in cancer patients after vaccination,although studies in murine models (Mizobata, S., K., et al., CancerImmunol. Immunother. 49:285-295 (2000); Morgan, D. J., et al., J.Immunol. 160:643-651 (1998)) and previous clinical trials (Cormier, J.N., et al., Cancer J. Sci. Am. 3:37-44 (1997); Salgaller, M. L., et al.,Cancer Res. 56:4749-4757 (1996); Wang, F., et al., Clin. Cancer Res.5:2756-2765 (1999); Muderspach, L., et al., Clin. Cancer Res.6:3406-3416 (2000); Weber, J. S., et al., J Immunother. 22:431-440(1999); Lee, P., et al., J. Clin. Oncol. 19:3836-3847 (2001)) havereported the absence of autoimmune toxicities associated with inductionof an anti-TAA CTL response. To address this important concern, apre-clinical immunopharmacology study was undertaken in HLA-A2.1/K^(b)transgenic mice to determine whether autoimmune pathological responsesoccur following in vivo immunization with EP-2101. Although not avalidated animal model for toxicological testing, this transgenic mousesystem offered the opportunity to assess this important safety issue ina pre-clinical setting since the HLA-A2.1/K^(b) transgene allowed forinduction of murine CTL responses against the human CTL epitopes in thevaccine (Wentworth, P. A., et al., Eur. J Immunol. 26:97-101 (1996);Vitiello, A., et al., J Exp. Med. 173:1007-1015 (1991)).

In this 18 week study, HLA-A2.1/K^(b) transgenic mice received a totalof six treatments with EP-2101 or a placebo emulsion control at threeweek intervals. Mice were injected at the tail base with EP-2101 at a150-fold excess dose on a mg/kg basis compared to the dose planned forcancer patients in the clinical trial. Histopathology was performed oninjected animals at three time points; at week two following a singletreatment, at week 9 after three treatments, and at week 18 after sixtreatments, on tissue from seven major organs (heart, lung, kidney,stomach, intestine, brain and liver) from each animal, as well as onskin isolated from the injection site. In addition to histopathology,animals were monitored at regular intervals for adverse events and bodyweight. Concurrent to histopathology analysis at the 3 time points andadverse event monitoring, the CTL responses in the spleen of vaccinatedand placebo-treated mice were also measured to correlate anyimmunopathology with presence of CTL responses against epitopes in thevaccine.

Results from this immunopharmacology study indicated that treatment withEP-2101 or an emulsion control did not result in autoimmuneimmunopathology in major organs of HLA-A2.1/K^(b) transgenic mice at allof the time points examined, even though strong CTL responses weredetected in animals. Histology sections of seven major organs fromanimals treated with EP-2101 or emulsion control appeared normal at allof the time points studied. The only pathology observed in this studyattributable to treatment was the appearance of granulomatousinflammation and granuloma formation at the injection site skin, whichappeared in both the vaccine and the emulsion control treatment groups.This observation is a common side-effect of treatment with theMontanide® ISA 51 adjuvant used in this study (Wang, F., et al., Clin.Cancer Res. 5:2756-2765 (1999); Lee, P., et al., J. Clin. Oncol.19:3836-3847 (2001); Leenaars, M., et al., Vet Imnzunol Immunopathol.61:291-304 (1998); Yamanaka, M., et al., J. Vet. Med. Sci. 54:685-692(1992)).

Adverse event monitoring of treated mice throughout the 18 week studyindicated an overall absence of symptomologies associated with illnessor toxicity, in both the vaccine and emulsion control-treated groups(e.g. lethargy, diarrhea, cachexia, paralysis, abnormal posture). Theonly observation of note was the appearance of a palpable lump at thetail base of all animals, consistent with granuloma formation, whichappeared transiently over a 2V2 week period between the 4th and 5thtreatment periods, in both the vaccine and emulsion control-treatedgroups. This transitory adverse event was not associated with necrosisor bleeding at the injection site skin, and such injuries were notobserved in any animal throughout the duration of the entire study.Finally, the absence of serious adverse events and immunopathology intest animals was confirmed by their body weight measurements whichappeared normal and increased steadily over the course of the study.

In summary, the absence of autoimmune inflammatory pathology in theHLA-A2.1/K^(b)) mouse model system observed in this current study isreminiscent of the absence of similar pathologies reported in previoushuman clinical trials where peptide vaccines formulated in Montanide®ISA 51 adjuvant were administered to cancer patients (Cormier, J. N., etal., Cancer J Sci. Am. 3:37-44 (1997); Salgaller, M. L., et al., CancerRes. 56:4749-4757 (1996); Wang, F., et al., Clin. Cancer Res.5:2756-2765 (1999); Muderspach, L., et al., Clin. Cancer Res.6:3406-3416 (2000); Weber, J. S., et al., J. Immunother. 22:431-440(1999); Lee, P., et al, J. Clin. Oncol. 19:3836-3847 (2001)). For theEP-2101 vaccine, the absence of autoimmune immunopathology inHLA-A2.1/K^(b) transgenic mice in the face of a broadly specific CTLresponse directed at multiple epitopes of self tumor antigens supportsthe general safety of administering this vaccine to colon and lungcancer patients in the proposed clinical trials.

Example 15 Clinical Trial

EP-2101 is a therapeutic, peptide vaccine for use as an adjuvant therapyin patients with cancer. The vaccine is designed for administration topatients for the induction of cytotoxic T lymphocytes (CTL) directedagainst carcinoembryonic antigen (CEA), p53, human epidermalreceptor-2/neurological (HER-2/neu) and melanoma antigen 2 and 3(MAGE-2/3), tumor associated antigens (TAAs) that are frequentlyover-expressed in colon and non-small cell lung cancer (NSCLC). Theclinical objective for inducing CTL responses against these fourwell-characterized TAAs is to delay or prevent the recurrence of cancerfollowing surgery, chemotherapy or radiation.

Cancer of the lung continues to be a major health problem with a veryhigh mortality rate. Approximately 170,000 new lung cancer cases werepredicted in the United States in 2001 and an estimated 160,000 patientsexpected to die from the disease. About 80% of lung cancers are NSCLC,and a majority of these patients present with later stage disease. The“standard of care” for NSCLC remains surgery, radiation therapy, orchemotherapy. In addition, some patients receive adjunctive therapyafter surgery in the form of chemotherapy following the removal ofdetectable tumor, although clinical studies are only now ongoing toassess the benefit of such treatment. Despite these treatments, the 2year survival rate is 30% for stage IIIa, 45% for IIb, 60% for IIa andIb and 80% for Ia. Mountain, C. Lung Cancer; A Handbook For Staging,Imaging and Lymph Node Classification (1999). Therefore, effectiveadjuvant therapies are critically needed.

The continued improvement in detection of colon cancers has enhanced theability to treat patients early in the course of disease. According tothe American Cancer Society, the five-year survival rate for localdisease is 91% while the survival rate for disseminated disease is only7% (American Cancer Society, Cancer Facts and FIGS. 2001). Projecteddeaths in the United States from colon cancer are approximately 50,000in 2001. The “standard of care” for stage D1 colon cancer is surgeryfollowed by chemotherapy utilizing 5-fluorouracil and leucovorin.Recently there has been increased use of irinotecan with 5-fluorouricland leucovorin in the adjuvant setting. Despite these availableregimens, additional safe and effective adjuvant treatments are needed.

EP-2101 is composed of ten synthetic peptides, each composed of 9-13amino acid residues, formulated as a stable water-in-oil emulsion inMontanide® ISA 51 adjuvant. Nine of the peptides represent Cat epitopes.Each CTL epitope is restricted by HLA-A2.1 and at least one other memberof the HLA-A2 superfamily of MHC class I molecules, providing coverageof approximately 45% of the general population. The CTL epitopesincluded represent a combination of wild-type, fixed-anchor analog andheteroclitic analog epitopes. The tenth synthetic peptide is a pan-DRepitope (PADRE®), a rationally-designed helper T lymphocyte (HTL)epitope included to augment the magnitude and duration of CTL responses.

The concept of inducing a CTL response to delay or prevent therecurrence of cancer is supported by significant animal model data,studies correlating tumor infiltration with a favorable clinical outcomeand reports of tumor regression following spontaneous or vaccine-inducedanti-tumor T cell responses (Yu, Z. and Restifo, N. P., J. Clin. Invest110:289-294 (2002)). Peptide epitopes have been utilized for theinduction of CTL responses in cancer patients in numerous clinicalstudies with some encouraging results (Rosenberg, S. A., et al., Nat.Med. 4:321-327 (1998); Fong, L., et al., Proc. Natl. Acad. Sci. USA98:8809-8814 (2001)). To improve the clinical outcome in the proposedstudies, the EP-2101 peptide vaccine was designed to incorporate theinsights and promising concepts learned from previous studies.Specifically, EP-2101 incorporates:

-   1. defined, optimal-length CTL epitopes derived from multiple,    well-characterized TAAs;-   2. epitopes with high HLA binding affinity and demonstrated ability    to induce CTL that recognize tumor cell lines;-   3. epitopes that are a mixture of wild-type sequences and two types    of analogs, fixed-anchor and heteroclitic, that were shown to induce    responses in humans that correlated with clinical responses;-   4. a rationally-designed, non-self, helper T cell PADRE® epitope,    that has been shown to induce helper responses in humans;-   5. Montanide® ISA 51, a mineral oil adjuvant similar to Incomplete    Freund's Adjuvant that is a well-characterized adjuvant for human    use that has exhibited acceptable safety and potency in numerous    clinical studies (Weber, J. S., et al, J Immunother. 22:431-440    (1999); Lee, P., et al., J. Clin. Oncol. 19:3836-3847 (2001);    Cormier, J. N., et al., Cancer J. Sci. Am. 3:37-44 (1997); Wang, F.,    et al., Clin. Cancer Res. 5:2756-2765 (1999); Muderspach, L., et    al., Clin Cancer Res. 6:3406-3416 (2000); Ressing, M. E., et al., J.    Immunother. 23:255-266 (2000); Yamshchikov, G. V., et al., Int J    Cancer 92:703-711 (2001); Rosenberg, S. A., et al., J Immunol.    163:1690-1695 (1999)).

The unique combination of wild-type and analog epitopes derived fromwell-studied TAAs and delivered in an adjuvant that has producedencouraging clinical data should provide an opportunity to improve onthe results obtained to date using peptide-based cancer vaccines.

Rationale for Dose Selection

EP-2101 is an immunotherapeutic vaccine consisting of nine peptideepitopes derived from four TAAs which stimulate CTL responses and thePADRE® universal helper T cell epitope. The 10 peptides are formulatedin an emulsion with Montanide® ISA 51 adjuvant which will beadministered to NSCLC and colon cancer patients to assess safety andimmunogenicity of the vaccine. Guidance as to the appropriate vaccinedosage for treating patients was provided by reports of previousclinical trials where CTL and clinical responses as well as vaccinesafety were reported following administration of a peptide/Montanide®ISA 51 vaccine (Weber, J. S., et al., J Immunother. 22:431-440 (1999);Lee, P., et al., J. Clin. Oncol. 19:3836-3847 (2001); Cormier, J. N., etal., Cancer J. Sci. Am. 3:37-44 (1997); Wang, F., et al., Clin. CancerRes. 5:2756-2765 (1999); Muderspach, L., et al., Clin. Cancer Res.6:3406-3416 (2000); Ressing, M. E., et al., J. Immunother. 23:255-266(2000); Yamshchikov, G. V., et al., Int J Cancer 92:703-711 (2001);Rosenberg, S. A., et al., J Immunol. 163:1690-1695 (1999)).

Several peptide vaccines formulated in Montanide® ISA 51 have beentested in cancer patients and these vaccines have generally been deemedsafe and well-tolerated with no severe dose-related systemic toxicitiesbeing reported (Weber, J. S., et al., J. Immunother. 22:431-440 (1999);Cormier, J. N., et al., Cancer J. Sci. Am. 3:37-44 (1997); Wang, F., etal., Clin. Cancer Res. 5:2756-2765 (1999); Muderspach, L., et al., Clin.Cancer Res. 6:3406-3416 (2000); Ressing, M. E., et al., J. Immunother.23:255-266 (2000)). The dose of peptide administered to patients inthese trials has been as high as 10 mg of total peptide per treatment,with most being in the range of 1-2 mg total peptide, and the treatmentschedule was similar to that being proposed for the EP-2101 clinicaltrial (i.e. 4-6 subcutaneous injections at 3-4 week intervals). The mostcommon toxicities reported were local injection site reactions (pain,tenderness, and granuloma formation) that were almost always scoredgrade 1 or 2 in severity (Wang, F., et al., Clin. Cancer Res.5:2756-2765 (1999); Muderspach, L., et al., Clin. Cancer Res.6:3406-3416 (2000); Ressing, M. E., et al., J. Immunother. 23:255-266(2000)). Other transient grade 1/2 toxicities that were occasionallyobserved included nausea, headaches, fever, and fatigue. Studies testingvaccines with more than a single peptide formulated in Montanide® ISA 51adjuvant include the clinical trials reported by Yamshchikov et al.(Yamshchikov, G. V., et al., Int J Cancer 92:703-711 (2001)) and Ressinget al. (Ressing, M. E., et al., J. Immunother. 23:255-266 (2000)). Ineach study, melanoma or cervical carcinoma patients were treated with amixture of three or five peptides, respectively, injected at doses up to3 mg total peptide. As observed in other studies, both vaccines showedonly limited grade 1/2 toxicities. Thus, collectively, data from theseclinical trials indicate that vaccines consisting of one or severalpeptide epitopes formulated in Montanide® ISA 51 at total peptide dosesup to 10 mg are generally well-tolerated.

With respect to induction of CTLs and clinical responses bypeptide/Montanide® ISA 51 vaccines, clinical trials examining escalatingdoses of peptide, ranging from 0.1 to 10 mg of peptide per injectiondose, have shown that CTL responses and clinical responses are inducedin this dose range, particularly at doses approaching 1 mg per peptideWeber, J. S., et al., J Immunother. 22:431-440 (1999); Cormier, J. N.,et al., Cancer J. Sci. Am. 3:37-44 (1997); Wang, F., et al., Clin.Cancer Res. 5:2756-2765 (1999); Muderspach, L., et al., Clin. CancerRes. 6:3406-3416 (2000))¹⁻⁴. For example, in a noteworthy studydescribed by Rosenberg et al. 7;8 (Rosenberg, S. A., et al., Nat. Med.4:321-327 (1998); Rosenberg, S. A., et J. Immunol. 163:1690-1695(1999)), where significant post-vaccination clinical responses werereported, a 1 mg dose of a single fixed-anchor analog peptide,gp100.209(210M), was delivered in Montanide® ISA 51. In this trial, a40% clinical response rate was observed in melanoma patients followingpeptide vaccination in conjunction with IL-2 therapy, compared to ahistorical response rate of 15% with IL-2 therapy alone (Rosenberg, S.A., et al., Nat. Med. 4:321-327 (1998)). Similarly, in another trialwhere a HPV-16 E7 peptide vaccine was tested in patients with high-gradecervical intraepithelial neoplasia, CTL responses and clinical responseswere reported at doses of 0.3 mg and 1 mg (Muderspach, L., et al., Clin.Cancer Res. 6:3406-3416 (2000)). With regard to correlating CTLinduction with peptide dose, Wang et al. (Wang, F., et al., Clin. CancerRes. 5:2756-2765 (1999)) observed that a high dose of theMelan-A/MART-1.27 peptide in Montanide® ISA 51 adjuvant (2 mgpeptide/dose) appeared to result in a greater magnitude of CTLresponses, as measured by interferon-gamma (IFN-γ) release using theenzyme-linked immunospot (ELISPOT) assay, when compared to patientsreceiving a lower dose (0.1 mg/dose). Although the number of patients inthis trial was limited, this finding is consistent with other studies inhumans immunized with a lipidated HBV CTL peptide construct (Vitiello,A., et al., J Clin. Invest 95:341-349 (1995)) or a tumor specificbcl-abl breakpoint peptide delivered in QS-21 adjuvant (Pinilla-Ibarz,J., et al., Blood 95:1781-1787 (2000))¹⁰ where higher doses of peptidewere shown to be more consistent at inducing T cell responses than lowerdoses.

A stable emulsion was generated at a 5 mg/ml total peptide dose (0.5mg/ml per peptide epitope). Thus, cancer patients in the EP-2101clinical trial will receive a dosage corresponding to 5 mg of totalpeptide (0.5 mg per epitope) in an injection volume of 1 ml. Patientswill receive six total subcutaneous injections at three week intervalsin an injection volume of 1 ml.

Potential risks of vaccine administration are known to the clinician ofordinary skill in the art and include discomfort at the site ofinjection, general symptoms associated with administration of a vaccine(chills, fever, rash, aches and pain, nausea, headache and fatigue);reproductive toxicity, anaphylactic reaction, effects on pregnancy andfetal development, and autoimmune reactions, including those of theretina.

Structural Formula

The amino acid sequence of each peptide is given in Tables 3 and 7.

Formulation of Dosage Form

EP-2101 is a sterile, preservative-free emulsion of 10 peptide epitopesat a concentration of 0.5 mg/ml each, formulated in Montanide® ISA 51adjuvant at a ratio of 1:1 (w:w) and filled into rubber-stoppered glassvials. The peptides are synthesized using standard Boc or Fmoc chemistryfor solid phase peptide synthesis starting with the appropriate resin,and purified by standard methods. The adjuvant is a mineral oiladjuvant, similar to Incomplete Freund's Adjuvant, manufactured andsupplied by Seppic, Inc., Fairfield, N.J. EP-2101 is manufactured underaseptic conditions. Peptides are dissolved in three different solvents,sterile filtered, pooled and then emulsified in adjuvant viahomogenization under controlled conditions.

Route of Administration

EP-2101 is designed for subcutaneous injection. The vaccine will beadministered as a 1 ml injection every three weeks for a total of sixinjections. The total peptide dose for each injection will be 5.0 mg(0.5 mg of each peptide).

Manufacture of Drug Substance

Peptides are prepared using solid phase synthesis methodology. Briefly,fluorenylmethoxycarbonyl (Fmoc) and/or tert-butyloxycarbonyl (Boc)groups are used as the protecting groups for the amino acid residues inthe synthesis. The peptide is built upon the appropriate resin.

Amino acid derivatives are added to the resin-based amino acid usingthree equivalents each of DIC and HOBt as the coupling reagents. TheFmoc or Boc protecting group is removed from the terminal amino acid ofthe resin-based peptide using 20% piperidine in DMF or 65% TFA indichloromethane, respectively.

The remaining Fmoc-N- or Boc-N-protected amino acid residues are addedto the resin-based peptide in sequential coupling cycles using DIC andHOBt as the coupling reagents and 20% piperidine in DMF or 65% TFA indichloromethane to remove Fmoc and Boc protecting groups, respectively.

Some side-chain protecting groups are removed using appropriate organicmixtures prior to peptide cleavage from the resin. Both removal ofadditional protecting groups and cleavage from the resin are achieved bytreatment of the peptide-resin with a mixture of hydrogenfluoride/methoxybenzene or TFA/water. The peptide is extracted from theresin with acetic acid and, in some cases, extraction withtrifluoroacetic acid. The resin is washed with ether. The peptide isisolated by lyophilization from the HOAc/TFA solution.

The peptide is purified by preparative Reverse Phase High Performance

Liquid Chromatography (RP-HPLC) on a C18 derivatized silica stationaryphase. The column is eluted and the fractions containing pure peptideare pooled and the peptide is isolated by Lyophilization. In some casesRP-HPLC is followed by ion exchange purification/deslating usingHOAc-buffered solvents. The resulting fractions are isolated bylyophilization.

Solubility of Individual Peptides

Solubility studies have been performed on the peptides, with solubilitydefined as a clear solution with no visible particulates (Table 8). Only6 out of 10 peptides (1013.08, 1243.08, 1295.03, 1323.06, 1350.01 and1352.03) were soluble at physiological pH. Therefore, the peptides weretested at 2-5 mg/ml in various aqueous acidic solutions and aqueousbasic solutions, in addition to dimethylsulfoxide (DMSO).

Specifications and Analytical Methods for the Drug Substance

Table 9 describes the specifications for the Drug Substance.

Components and Quantitative Composition

The components and quantitative composition of EP-2101 are described inTable 10.

Component Specifications

The components used in the manufacture of the drug product are listed inTable 11.

Method of Manufacture of the Bulk Drug Product and Drug Product

The bulk drug product is prepared as shown in FIG. 5. The bulk drugproduct is formulated into three solutions (see Tables 8 and 12) basedon the solubility of individual peptides in each of the three solventsand the solubility of the peptides when pooled. Briefly, to allow foraseptic processing, the 10 peptides are dissolved into either an acidicsolution (0.1875 M acetic acid), a basic solution (0.1 M sodiumhydroxide) or the organic solvent DMSO. These three peptide-containingpools are sterilized by filtration. Under aseptic conditions, thesethree peptide pools are combined, buffered, pH adjusted and thenhomogenized with Montanide® ISA 51 adjuvant under temperature-controlledconditions to form the drug product. The drug product, a stable 1:1(w:w) emulsion, is then filled into 2 ml glass vials and stored at 2-8°C.

Drug Product Specifications and Analytical Methods

Tables 13 and 14 describe the specifications for EP-2101 bulk drugproduct and drug product, respectively.

Peptide Concentration (Each Peptide)

Concentration of all peptide components in the EP-2101 Drug Product isassayed by RP-HPLC (conditions illustrated in Table 15). A specifiedquantity of the emulsion is mixed with a solution of 0.1% TFA in DMSO toform a two-layered mixture. Attempts to produce a clear, homogeneoussolution for HPLC analysis by using solvents other than DMSO wereunsuccessful. Sampling of the aforementioned two-phase mixture takesplace by inserting a syringe or pipette through the top mineral oillayer and into the bottom, DMSO layer. The only sample taken for HPLCanalysis is taken from the DMSO layer, in which all peptides aresoluble. HPLC chromatography affords a distinct chromatographic peak foreach peptide, which upon integration and comparison to a calibrationcurve yields the individual peptide concentration in the EP-2101 DrugProduct. The biphasic nature of the sample introduces variability in theestimation of the full sample volume as well as the transfer of thesample. Subsequently, because of the complexity of sample preparationand handling, unusually large errors in determining the peptideconcentration (as high as 30%) were observed. The large variability wasnot accompanied by major degradation product formation or other unusualphysical changes of the sample, and is inferred to be a result of samplepreparation and handling. For this reason the specification of ±50% ofthe intended concentration was set as a release and stability criterion.Attempts to improve the sample handling and, simplify the biphasicmineral oil-DMSO mixture are currently underway with a primary aim ofnarrowing the release and stability specifications.

Potency

EP-2101 is composed of synthetic CTL and HTL peptide epitopes. Peptidecontent and integrity can be determined accurately by physical/chemicalcharacterization using the analytical methods described above (e.g.HPLC, viscosity, and particle size analysis). In addition, a method forevaluating the overall potency of the drug product has been developed.

Development of a relevant potency assay is challenging because theEP-2101 vaccine is designed to specifically stimulateHLA-A2.1-restricted CTL responses in humans and not other species. Oneway to address this challenge is to measure the in vivo potency ofEP-2101 using mice that express the HLA-A2.1 molecule as a transgene(i.e. HLA-A2.1/K^(b) transgenic mice). The proposed EP-2101 potencyassay is similar to the preclinical assay used to measure theimmunogenicity of EP-2101 CTL epitopes in HLA-A2.1/K^(b) transgenic mice(see Example 13). It should be pointed out that the HLA-A2.1/K^(b)transgenic mouse assay has limitations in quantifying CTL responses,specifically: 1) only about 80% of the HLA-A2.1-restricted epitopes thatare immunogenic in humans also induce CTL responses in transgenic mice(Wentworth, P. A., et al., Eur. J. Immunol. 26:97-101 (1996)),therefore, CTL responses against some epitopes cannot be quantifiedusing this system, and; 2) using a number of approaches, we have foundthat in vivo CTL responses generated in HLA transgenic mice, whetherinduced by vaccination or natural infection, are variable fromexperiment-to-experiment due to individual animal differences and to thein vitro manipulation of primed T cells required for this assay method(e.g. see FIG. 7). Although the potency assay has limitations common toin vivo bioassays, it provides a measurement of overall potency ofEP-2101. Accordingly, it serves as an appropriate complement to thehighly sensitive and quantitative analytical assays described above.

In the EP-2101 potency assay, HLA-A2.1/K^(b) transgenic mice areinjected with EP-2101 and 14 days later splenocytes from immunizedanimals are stimulated in vitro with representative EP-2101 CTLepitopes, CEA.691H5 (1352.02) and HER-2/neu.369V2V9 (1334.10), to expandin vivo-primed CTL. Following in vitro expansion, in vivo-primed CTLresponses (also referred to as effector cells) will be quantitated bymeasuring, with an ELISA, their capacity to produce IFN-γ whenstimulated again in vitro with the CEA.691H5 or HER-2/neu.369V2V9peptides. CTL activity measured by ELISA is expressed as secretory units(SU), which represent the number of effector cells needed to secrete 100pg of IFN-γ in response to peptide (McKinney, D. M., et al., J. Immunol.Methods 237:105-117 (2000)). Thus, the SU value is a reflection of thelevel of CTL induced by EP-2101 in HLA-A2.1/K^(b) transgenic mice and isa measurement of vaccine potency.

Example 16 Detailed Description of the Potency Assay

To assess the drug potency, an assay has been developed to measure theability of the vaccine to induce a CTL response in transgenic mice thatexpress a chimeric MHC class I molecule in which the heavy chain iscomposed of the first and second domains of the HLA-A2.1 molecule andthe third domain, transmembrane domain, and cytoplasmic domain of themouse H-2K^(b) molecule. Previously, it was demonstrated that whenHLA-A2.1/K^(b) transgenic mice are immunized with HLA-A2.1-restrictedepitopes known to be immunogenic in humans, approximately 80% of theepitopes induce CTL responses (Wentworth, P. A., et al., Eur. J.Immunol. 26:97-101 (1996)). These data confirm the validity of usingthese mice to quantitate CTL responses induced upon immunization with avaccine composed of HLA-A2.1restricted epitopes.

The selection of two CTL epitopes for measuring EP-2101 potency and theestablishment of a potency assay specification is described below.Specific protocols are described in Example 17.

Briefly, analysis of the immunogenicity of EP-2101 in severalexperiments indicated that the different epitopes in the vaccine inducedvarying responses ranging from a mean of ˜10 SU to >100 SU and theseresponses were associated with high intra- and inter-experimentalvariability, particularly for weakly immunogenic epitopes. Both of thesefactors made it unfeasible to measure potency of the vaccine based onCTL responses against all nine epitopes in the vaccine. Instead, anassay was developed using the immunogenicity measurements of tworepresentative, immunogenic epitopes in EP-2101 as an indicator ofoverall vaccine potency.

Selection of the two epitopes was based on a retrospective analysis ofCTL immunogenicity data generated from experiments where mice wereinjected with EP-2101 at varying emulsion doses. CTL responses from 6-10independent experiments in which mice were immunized with a 10 mg/mlemulsion dose were evaluated and the two top immunogenic epitopes inEP-2101 were CEA.691H5 (geometric mean response, 164×/÷1.8 SU) andHER-2/neu.369V2V9 (geometric mean response, 152 ×/÷2.4 SU), with a thirdepitope, MAGE-3.11215 (geometric mean response, 92×/÷2.1 SU) serving asa potential back-up epitope. In addition to the high response magnitude,the overall variability associated with these responses was withinranges normally observed for immunogenic epitopes tested inHLA-A2.1/K^(b) transgenic mice (SD between ×/÷ 1.8-2.4). Although thisextensive database was generated with EP-2101 at a 10 mg/ml emulsiondose, further experiments indicate that the EP-2101 emulsions at a 2.5mg/ml and 5 mg/ml total peptide dose induce a comparable level of CTLresponse as the 10 mg/ml emulsion dose against the highly immunogenicCEA.691H5, HER-2/neu.369V2V9, and MAGE-3.11215 epitopes.

Further support for epitope selection was provided by data fromresponses-measured in the ELISPOT assay which tests for CTL effectorcell activity without in vitro expansion by peptide stimulation.Consistent CTL responses could be detected by the ELISPOT assay againstthe HER-2/neu.369V2V9 and CEA.691H5 epitopes and these results confirmthe strong immunogenicity of the two candidate potency assay epitopescompared to others in the vaccine when tested with this assay.

In addition to responses measured in immunized mice, the baseline CTLresponses observed in naïve mice or in mice injected with a placeboMontanide® ISA 51 emulsion were also considered. For the three topepitope candidates, CTL responses in negative control mice in threeindependent experiments were low (<10 SU), such that the difference inthe magnitude between the baseline and vaccine-induced CTL responses wassufficiently large to assure detection of a drop in vaccine potencyshould it occur after manufacture.

A final consideration in epitope selection for the potency assay wasvariability of CTL induction associated with individual mice. Since theprotocol for the EP-2101 potency assay specifies measurement of CTLresponses in a pooled splenocyte population derived from 6 immunizedmice, a potential source of variability in the assay could be thefrequency of CTL induction in individual animals. This consideration isnot trivial since sporadic CTL responses behaving in an all-or-nonefashion have been observed in individual mice injected with differenttypes of highly immunogenic vaccine constructs (e.g. lipopeptide, DNA)(unpublished results). In light of this important parameter, a study wasinitiated to determine the variability of CTL induction against the topthree potency. epitope candidates in 15 individual HLA-A2.1/K^(b)transgenic mice immunized with the EP-2101 vaccine. CTL responsesagainst all three epitopes could be demonstrated in 100% of theimmunized animals. As expected, the hierarchy of CTL responses againsteach of the three epitopes was similar to that measured with a pool ofsplenocytes from primed mice and the degree of variability of theresponses between individual animals was within an acceptable range foran in vivo assay. Thus, CEA.691H5 and HER-2/neu.369V2V9 induced the mostrobust and reproducible CTL response in all animals, followed by theMAGE-3.11215 epitope (geometric mean SU response in 15 mice against theCEA, HER-2/neu, and MAGE-3 epitopes was 252×/÷ 1.4, 169×/÷1.7, and 48×/÷1.7, respectively and these responses were within the range observedwith pooled splenocytes from EP-2101-immunized animals).

In summary, the CEA.691H5 and HER-2/neu.369V2V9 epitopes were selectedas the potency assay epitopes, and the MAGE-3.11215 epitope wasdesignated as a back-up based on 1) the strength of CTL responsesmeasured in EP-2101 immunized animals using the in situ ELISA and exvivo ELISPOT assays, 2) the equivalent magnitude of CTL responsesgenerated against the epitopes with EP-2101 vaccine formulated atvarying peptide emulsion doses, 3) the inter- and intra-experimentvariability of these CTL responses, 4) the baseline responses innegative control animals, and 5) the consistency of CTL induction inindividual animals.

A potency assay specification was established to determine the upper andlower limits of CTL responses against the two potency epitopes inducedby EP-2101. To establish the lower specification limit, the data-basegenerated in naïve or emulsion control (placebo) mice over sixexperiments (18 data-points) was analyzed and the SU values of allcultures from negative control mice were compiled. The lower limitspecification was established by first calculating the geometric mean SUresponse and SD from all of the negative control cultures and thencalculating a 3 SD cutoff value. This value for the CEA.691H5 epitopewas calculated to be 22 SU (geometric mean×3 SD=1.53×14.01; withrounding to the next highest integer) and 8 SU for the HER-2/neu.369V2V9epitope (geometric mean×3 SD=0.49×14.58). For a given test sample ofEP-2101 to pass potency, the geometric mean SU value of CTL activityfrom EP-2101-primed splenocytes for both epitopes must equal or exceedits respective lower limit specification.

To establish the upper limit of the assay, SU values from 11 experiments(32 data-points) generated from EP-2101-injected mice were compiled andthe geometric mean SU value from the three highest experiments for eachepitope was calculated. For the CEA.691H5 epitope, this calculationresulted in a value of 289.5 SU based on the responses of individualcultures from three experiments. For HER-2/neu.369V2V9, the geometricmean SU of the three highest responding experiments was 330.9 SU. Sincein vivo biological responses in vaccine-immunized subjects tend togenerate significant differences at log intervals of dosage (Vitiello,A., et al., J. Clin. Invest. 95:341-349 (1995); Pinilla-Ibarz, J., etal., Blood 95:1781-1787 (2000)), a log greater CTL response value fromthe mean of the highest responses observed in EP-2101-immunized animalswas established as the upper limit specification. Thus, the upper limitspecification for the two epitopes was determined by multiplying thegeometric mean SU value of the three highest experiments by 10 thenrounding this value. For CEA.691H5 this value was calculated to be 2,895SU or 2,900 SU and for the HER-2/neu epitope the same calculationyielded a value of 3,309 SU or 3,300 SU. A given test sample of EP-2101which exceeds the upper limit specification of 2,900 SU and 3,300 SU forthe CEA.691H5 and HER-2/neu.369V2V9 epitopes respectively, fails thepotency assay due to concerns regarding super-optimal CTL inducingactivity and potential toxicity.

Each potency experiment will also include system suitability controlswhich will determine the validity of the EP-2101 potency measurements,obtained in the experiment. As a positive control, mice will beco-immunized with each CTL epitope alone and the PADRE® epitope in aMontanide® ISA 51 emulsion and CM responses in this group will bemonitored using the same specifications established for the EP-2101vaccine product. As a negative control, splenocytes from naïve(non-vaccinated) mice will be stimulated in vitro with each CTL epitopeunder identical conditions as splenocytes harvested fromEP-2101-immunized mice and as a criteria for a valid potency assay, CTLresponses in this control group should not exceed the lowerspecification limit for each epitope.

Example 17 Detailed Protocols Mice

HLA-A2.1/K^(b) transgenic mice were generated as described previously(Vitiello A., et al., J. Exp. Med. 173:1007-15 (1991)) as an F1generation of a cross between an HLA-A2.1/K^(b) transgenic straingenerated on the C57/BL6 background and BALB/c mice.

Cell Culture Medium

All cells were grown in RPMI-1640 medium with HEPES (Life Technologies,Grand Island, N.Y.) supplemented with 10% FBS, 4 mM L-glutamine, 5×10⁻⁵M 2-ME, 0.5 mM sodium pyruvate, 1× non-essential amino acid residues,100 μ g/ml streptomycin and 100 U/ml penicillin (hereafter designatedRPMI-10 medium).

Preparation of Montanide ISA 51 Peptide Emulsions

For emulsion preparations, the individual peptides in the EP-2101vaccine were solubilized from a lyophilized powder in the appropriateaqueous or DMSO solution and at the appropriate concentrations to yield10, 5, or 2.5 mg/ml total peptide in the final adjuvant emulsion. Thedifferent solutions, the respective peptides formulated in them, and themethod of formulation are described below.

Solution 1 (Acidic Pool): Peptides CEA.691H5, p53.149M2, MAGE3.11215,and PADRE were solubilized in 0.1875M acetic acid. The CEA.691H5 peptidewas solubilized first by 2 minutes of vortexing at high speed, followedby 5-10 minutes of sonication (35-40° C.). The other peptides were addedone at a time and solubilized by vortexing for 1-2 minutes.Solution 2 (Basic Pool): Peptides CEA.24V9, CEA.605D6, HER2.689,MAGE2.157, and p53.139L2B3 were solubilized in 0.1M NaOH. Peptides werereadily solubilized with brief vortexing (1-2 minutes).Solution 3 (DMSO): Peptide HER2.369V2V9 was solubilized in DMSO withvortexing (2 minutes) and heating (35-40° C.).

All Solutions were stored at 4° C. until they were combined to generatePool 4 which contains a mixture of all 10 peptides.

Pool 4 (Combination of Solutions 1, 2, and 3): Solutions 1, 2 and 3 werecombined in a 4:5:1 ratio (v:v, e.g. 0.8:1:0.2 ml respectively), or in a3.2:4:1 ratio (v:v, e.g. 0.8: 1: 0.25 ml respectively), which resultedin precipitation of some peptides. The combined pool was buffered with0.2 ml of 62.5 mM sodium phosphate (pH 7) and pH-adjusted to pH 7 with0.5 M NaOH (approximately 178 μl per 2.5 ml of final pool 4 afterbuffering and water addition), then brought to volume (2.5 ml) withwater-for-injection (WFI).

The final Pool 4 solution was then combined 1:1 v:v with Montanide® ISA51 (Seppic Inc.) and emulsified by homogenization using a Silverson L4RThomogenizer fitted with a ⅜ inch mini-micro tubular probe. Typically, a10 mg/ml research emulsion was prepared in a total volume of 1.5˜5 ml,with the tube kept cool on ice during preparation. Initially, the probewas carefully inserted into the oil layer near the water/oil interfaceand the oil layer was mixed at a low speed before the probe wastransferred to the bottom of the tube and the speed adjusted to 8,000rpm. Homogenization was performed for a total of 30 minutes and an evenemulsion was produced by repeatedly raising and lowering the tube duringthis interval. The final EP-2101 emulsified product was kept at 4° C.,prior to injection of animals.

Emulsions at a 2.5 mg/ml and 5 mg/ml total peptide dose were prepared ata scale of approximately 25 ml, 500 ml, or 1 liter using probes andmixing screens of appropriate diameter and pore size.

Placebo emulsion (emulsion control) was prepared as described above,except Solutions 1, 2, and 3 did not contain peptides.

Immunization of Mice and In Vitro Expansion of In Vivo-Primed CTLs

HLA-A2.1/K^(b) transgenic mice were immunized with EP-2101 or placeboemulsion subcutaneously at the tail base in an injection volume of50-100 μl/animal. Eleven to fourteen days after immunization, animalsfrom each experimental group were sacrificed and a single cellsuspension was prepared from a pool of mouse spleens. Individualcultures of splenocytes (20-25×10⁶ cells per culture) were thenstimulated in vitro in upright 25 cm² flasks with individual CTLepitopes represented in EP-2101 (1 μg/ml final peptide concentration in10 ml of RPMI-10 medium; duplicate or triplicate cultures establishedper epitope). As APCs, 1-1.25×10⁷ irradiated (4000 rad) LPS-activatedblasts were added to each culture. LPS blasts were prepared bystimulating spleen cells from untreated HLA-A2.1/K^(b) mice in vitrowith 6.25 μg/ml LPS (Sigma Chemical Co., St. Louis, Mo.) and 7 μg/mldextran sulfate (500,000 M. W., 17% sulfur, Pharmacia BioprocessTechnology, Uppsala, Sweden) for 3 days at 37° C.

Splenocyte cultures stimulated with EP-2101 peptide were incubated for 6days at 37° C. in 5% CO₂ before each culture was measured for CTLactivity using the IFN-γ in situ ELISA, as described below.

Measurement of CTL Activity

Six days after initiation of culture, CTL activity from individualcultures was measured by the IFN-γ in situ ELISA as previously described(McKinney, D. M, et al., J Immunol Methods 237:105 (2000)). Briefly, CTLeffector cells (4×10⁵) cells were added to 4 or 6 wells in a 96-wellplate (flat-bottom, precoated with a capture anti-IFN-γ monoclonalantibody). Cells were then serially diluted 4-fold in RPMI-10 mediumuntil a final concentration of 391 cells/well was achieved.Jurkat-A2.1/K^(b) tumor cells (10⁵/well) were then added to each well.Half of the wells in each replicate (cells were plated in replicates of6 or 4 wells) received 10 μg/ml of CTL peptide and the remaining wellsreceived medium. After overnight incubation, wells were washed anddeveloped to determine IFN-γ content by sequential treatment with asecondary biotinylated anti-IFN-γ monoclonal antibody, streptavidinperoxidase, and finally substrate. The pg of IFN-γ released per well byCTLs in the presence or absence of peptide was calculated by measuringabsorbance with an automated ELISA reader and extrapolating the IFN-γconcentration from a standard curve. The data is expressed in secretoryunits (SU) as calculated by the method described by McKinney et al.(McKinney, D. M, et al., J Immunol Methods 237:105 (2000)). Onesecretory unit is defined as the release of 100 pg/well of IFN-γ by 10⁶effector cells.

Measurement of CTL and HTL Induction by the ELISPOT Assay

ELISPOT assays to measure CTL or HTL responses induced by EP-2101 wereperformed according to previously published protocols (Lewis J J, etal., Int J Cancer 87:391 (1998)). Briefly, flat bottom 96-wellnitrocellulose plates (IP, Millipore) were coated with IFN-γ mAb (10μg/ml, clone R4-6A2, PharMingen) and incubated overnight at 4° C. Afterwashing with PBS, plates were blocked with RPMI-10 medium for 1 h at 37°C. Four×10⁵ CD8⁺ cells or CD4⁺ cells (isolated with Miltenyi isolationsystem from EP-2101-immunized splenocytes) and 5×10⁴ Jurkat-A2.1/K^(b)cells (for CD8⁺ cells) or 10⁵ γ-irradiated naïve spleen cells (for CD4⁺cells, treated with erythrocyte lysis buffer) were added to each well.Wells also received 10 μg/ml of CTL or HTL peptide to test for inductionof responses against EP-2101 epitopes or an identical concentration ofan irrelevant peptide. The irrelevant peptide for the CD8 ELISPOT assaywas the HCV core.132 peptide (DLMGYIPLV (SEQ ID NO: )) and the HCVNS3.1253 peptide (GYKVLVLNPSVAATL (SEQ ID NO: )) for the CD4 ELISPOTassay. After incubation, the plates were washed thoroughly withPBS/0.05% Tween 20 and biotinylated IFN-γ mAb (2 μg/ml, clone XMG1.2,PharMingen) was added to each well and incubated for 2-4 h at 37° C.After washing 4 times with PBS/0.05% Tween 20, Vectastain ABC peroxidase(Vectastain Elite kit; Vector laboratories, Inc., Burlingame, Calif.,USA) was added to the wells and plates were incubated for 1 h at roomtemperature. The plates were washed again 3 times with PBS/0.05% Tween20 followed by 3 washes with PBS. One hundred μl of AEC solution (SigmaChemical Co) was added to develop the spots. The reaction was stoppedafter 4-6 minutes under running tap water. The spots were counted bycomputer-assisted image analysis (Zeiss KS ELISPOT Reader, Jena,Germany). The net number of spots/10⁶ CD8⁺cells or CD4⁺cells wascalculated as (number of spots against relevant peptide)−(number ofspots with irrelevant control peptide)×2.5.

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, patentapplications and sequence listings cited herein are hereby incorporatedby reference in their entirety for all purposes.

TABLE 1 Sequence of Peptides in Drug Substance Peptide IdentificationSequence Epitope Type 965.10 aKXVAAWTLKAAa pADRE® Universal Helper TCell Epitope 1013.08 RLLQETELV HER-2/neu.689 Wild-type 1090.01YLQLVFGIEV MAGE2.157 Wild-type 1243.08 LLTFWNPPV CEA.24V9 Fixed-AnchorAnalog 1295.03 SMPPPGTRV p53.149M2 Fixed-Anchor Analog 1323.06 KLBPVQLWVp53.139L2B3 Fixed-Anchor Analog 1334.10 KVFGSLAFV HER-2/neu.369V2V9Fixed-Anchor Analog 1350.01 YLSGADLNL CEA.605D6 Heterocltic Analog1352.02 IMIGHLVGV CBA.691H5 Heterocltic Analog 1352.03 KVAEIVHFLMAGE-3.112I5 Heteroclitic Analog a = d-alanine, B = α-aminoisobutyricacid, X = cyclohexylalanine

TABLE 2 Overview of current cancer vaccine approaches. APPROACHDESCRIPTION ISSUES STRENGTHS Whole Cell Involve the administration ofOften difficult to Likely to have Vaccines whole cancer cells withobtain tumor cells novel TAA adjuvants which serve to Patientvariability potentiate the immune response Single patient product Hasrelatively low concentration of relevant TAA epitopes Cell LysateConsist of lysed allogeneic Often difficult to Likely to have Vaccinescancer cell membrane particles obtain tumor cells novel TAA that areingested by macrophages Patient variability and presented as tumorantigens Single patient product to effector cells Has relatively lowconcentration of relevant TAA epitopes Idiotypic Contain proteinsderived from Often difficult to Specific TAA Vaccines individual patienttumors or from obtain tumor cells specific tumor types Patientvariability Single patient product Has relatively low concentration ofrelevant TAA epitopes Whole Limited disease Complex Antigen coverage“natural” Vaccines Difficult to break immune tolerance responses may beelicited Relatively easy single compound manufacture Viral Consist ofvaccinia virus Often difficult to oncolysate infected cancer cell, lysedto obtain tumor cells vaccines form membrane segments Not alwayspossible expressing both vaccinia and to infect cancer cells cancer cellantigens Patient specific treatment Has relatively low concentration ofrelevant TAA epitopes Shed antigen Similar to whole cell and lysateDifficult to purify Likely to have vaccines vaccines but are partiallyantigens novel TAA purified Patient specific treatment Has relativelylow concentration of relevant TAA epitopes Genetically A number ofavenues are being Very difficult to Cells contain modified exploredincluding the obtain tumor tissues novel TAA tumor cell transduction ofcells with GM- and grow to allow and adjuvants vaccines CSF stabletransduction Patient specific treatment Peptide Synthetic peptides areproduced Need to choose Single Vaccines that correspond to tumor correctpeptides to preparation associated antigens. Designed to elicit aneffective used for stimulate a cytotoxic T-Cell immune response multipleresponse (CTL) Restriction to HLA patients and subtype or HLA possiblysupertypes multiple diseases Possible to combine various antigens/targets Reproducible antigen production Able to break tolerance Able toelicit responses to subdominant epitopes Can be directed to supertypesfor broad population coverage Carbohydrate Synthetically produced tumorMay need CTL Single vaccines associated carbohydrates, response as wellas preparation designed to stimulate an humoral response used forantibody response against the Carbohydrate multiple carbohydrateantigens antigens are HTL patients and dependent possibly multiplediseases

TABLE 3 POSITION POSITION POSITION C Terminus (Primary 2 (PrimaryAnchor) 3 (Primary Anchor) Anchor) SUPERMOTIFS A1 T, I, L, V, M, S F, W,Y A2 L, I, V, M, A, T, Q I, V, M, A, T, L A3 V, S, M, A, T, L, I R, KA24 Y, F, W, I, V, L, M, T F, I, Y, W, L, M B7 P V, I, L, F, M, W, Y, AB27 R, H, K F, Y, L, W, M, I, V, A B44 E, D F, W, L, I, M, V, A B58 A,T, S F, W, Y, L, I, V, M, A B62 Q, L, I, V, M, P F, W, Y, M, I, V, L, AMOTIFS A1 T, S, M Y A1 D, E, A, S Y A2.1 L, M, V, Q, I, A, T V, L, I, M,A, T A3 L, M, V, I, S, A, T, F, K, Y, R, H, F, A C, G, D A11 V, T, M, L,I, S, A, K, R, Y, H G, N, C, D, F A24 Y, F, W, M F, L, I, W A*3101 M, V,T, A, LP, I, S R, K A*3301 M, V, A, L, F, I, S, T R, K A*6801 A, V, T,M, S, L, I R, K B*0702 P L, M, F, W, Y, A, I, V B*3501 P L, M, F, W, Y,I, V, A B51 P L, I, V, F, W, Y, A, M B*5301 P I, M, F, W, Y, A, L, VB*5401 P A, T, I, V, L, M, F, W, Y

Bolded residues are preferred, italicized residues are less preferred: Apeptide is considered motif-bearing if it has primary anchors at eachprimary anchor position for a motif or supermotif as specified in theabove table.

TABLE 3a POSITION POSITION POSITION 2 (Primary Anchor) 3 (PrimaryAnchor) C Terminus (Primary Anchor) SUPERMOTIFS A1 T, I, L, V, M, S F,W, Y A2 V, Q, A, T I, V, L, M, A, T A3 V, S, M, A, T, L, I R, K A24 Y,F, W, I, V, L, M, T F, I, Y, W, L, M B7 P V, I, L, F, M, W, Y, A B27 R,H, K F, Y, L, W, M, I, V, A B58 A, T, S F, W, Y, L, I, V, M, A B62 Q, L,I, V, M, P F, W, Y, M, I, V, L, A MOTIFS A1 T, S, M Y A1 D, E, A, S YA2.1 V, Q, A, T* V, L, I, M, A, T A3.2 L, M, V, I, S, A, T, F, K, Y, R,H, F, A C, G, D A11 V, T, M, L, I, S, A, K, R, H, Y G, N, C, D, F A24 Y,F, W F, L, I, W *If 2 is V, or Q, the C-term is not L

Bolded residues are preferred, italicized residues are less preferred: Apeptide is considered motif-bearing if it has primary anchors at eachprimary anchor position for a motif or supermotif as specified in theabove table.

TABLE 4 POSITION 1 2 3 4 5 6 7 8 C-terminus SUPER MOTIFS A1 1° Anchor 1°Anchor T, I, L, V, M, S F, W, Y A2 1° Anchor 1° Anchor L, I, V, M, A, L,I, V, M, A, T T, Q A3 preferred 1° Anchor Y, F, W, (4/5) Y, F, W, Y, F,W, (4/5) P, (4/5) 1°Anchor V, S, M, A, T, (3/5) R, K L, I deleterious D,E (3/5); P, (5/5) D, E, (4/5) 1° Anchor 1° Anchor A24 Y, F, W, I, V, F,I, Y, W, L, M L, M, T B7 preferred F, W, Y (5/5) 1°Anchor F, W, Y (4/5)F, W, Y, 1°Anchor L, I, V, M, (3/5) P (3/5) V, I, L, F, M, W, Y, Adeleterious D, E (3/5); P (5/5); D, E, (3/5) G, (4/5) Q, N, (4/5) D, E,(4/5) G (4/5); A (3/5); Q, N, (3/5) 1° Anchor 1° Anchor B27 R, H, K F,Y, L, W, M, V, A 1° Anchor 1° Anchor B44 E, D F, W, Y, L, I, M, V, A 1°Anchor 1° Anchor POSITION 9 or C- 1 2 3 4 5 6 7 8 C-terminus terminusB58 A, T, S F, W, Y, L, I, V, M, A 1° Anchor 1° Anchor B62 Q, L, I, V,M, P F, W, Y, M, I, V, L, A MOTIFS A1 preferred G, F, Y, W, 1°Anchor D,E, A, Y, F, W, P, D, E, Q, N, Y, F, W, 1°Anchor 9-mer S, T, M, Ydeleterious D, E, R, H, K, L, I, V A, G, A, M, P, A1 preferred G, R, H,K A, S, T, C, L, I 1°Anchor G, S, T, C, A, S, T, C, L, I, V, M, D, E,1°Anchor 9-mer V, M, D, E, A, S Y deleterious A R, H, K, D, E, D, E, P,Q, N, R, H, K, P, G, G, P, P, Y, F, W, A1 peferred Y, F, W, 1°Anchor D,E, A, Q, N, A, Y, F, W, Q, N, P, A, S, T, C, G, D, E, P, 1°Anchor 10-merS, T, M Y deleterious G, P, R, H, K, G, L, I D, E, R, H, K, Q, N, A R,H, K, Y, F, W, R, H, K, A V, M, A1 preferred Y, F, W, S, T, C, L, I, V1°Anchor A, Y, F, W, P, G, G, Y, F, W, 1°Anchor 10-mer M, D, E, A, S Ydeleterious R, H, K, R, H, K, D, E, P, G, P, R, H, K, Q, N, P, Y, F, W,A2.1 preferred Y, F, W, 1°Anchor Y, F, W, S, T, C, Y, F, W, A, P1°Anchor 9-mer L, M, I, V, Q, V, L, I, M, A, T A, T deleterious D, E, P,D, E, R, K, H R, K, H D, E, R, K, H A2.1 preferred A, Y, F, W, 1°AnchorL, V, I, M, G, G, F, Y, W, L, 1°Anchor 10-mer L, M, I, V, Q, V, I, M, V,L, I, M, A, T A, T deleterious D, E, P, D, E, R, K, H, A, P, R, K, H, D,E, R, K, R, K, H, H, A3 preferred R, H, K, 1°Anchor Y, F, W, P, R, H, K,Y, A, Y, F, W, P, 1°Anchor L, M, V, I, S, F, W, K, Y, R, H, F, A A, T,F, C, G D deleterious D, E, P, D, E A11 preferred A, 1°Anchor Y, F, W,Y, F, W, A, Y, F, W, Y, F, W, P, 1°Anchor V, T, L, M, I, K,, RY, H S, A,G, N, C, D, F deleterious D, E, P, A G, A24 preferred Y, F, W, R, H, K,1°Anchor S, T, C Y, F, W, Y, F, W, 1°Anchor 9-mer Y, F, W, M F, L, I, Wdeleterious D, E, G, D, E, G, Q, N, P, D, E, R, H, K, G, A, Q, N, A24preferred 1°Anchor P, Y, F, W, P, P, 1°Anchor 10-mer Y, F, W, M F, L, I,W deleterious G, D, E Q, N R, H, K D, E A Q, N, D, E, A, A3101 preferredR, H, K, 1°Anchor Y, F, W, P, Y, F, W, Y, F, W, A, P, 1°Anchor M, V, T,A, L, R, K I, S deleterious D, E, P, D, E, A, D, E, D, E, D, E, D, E,A3301 preferred 1°Anchor Y, F, W A, Y, F, W 1°Anchor M, V, A, L, F, R, KI, S, T deleterious G, P D, E A6801 preferred Y, F, W, S, T, C, 1°AnchorY, F, W, L, I, Y, F, W, P, 1°Anchor A, V, T, M, S V, M R, K L, Ideleterious G, P, D, E, G, R, H, K, A, B0702 preferred R, H, K, F, W, Y,1°Anchor R, H, K, R, H, K, R, H, K, R, H, K, P, A, 1°Anchor P L, M, F,W, Y, A, I, V deleterious D, E, Q, N, P, D, E, P, D, E, D, E, G, D, E,Q, N, D, E, B3501 preferred F, W, Y, L, I, V, M, 1°Anchor F, W, Y, F, W,Y, 1°Anchor P L, M, F, W, Y, I V, A deleterious A, G, P, G, G, B51preferred L, I, V, M, F, W, Y, 1°Anchor F, W, Y, S, T, C, F, W, Y, G, F,W, Y, 1°Anchor P L, I, V, F, W Y, A, M deleterious A, G, P, D, E, R, H,K, D, E, G, D, E, Q, N, G, D, E, S, T, C, B5301 preferred L, I, V, M, F,W, Y, 1°Anchor F, W, Y, S, T, C, F, W, Y, L, I, V, M, F, F, W, Y,1°Anchor P W, Y, I, M, F, W, Y, A, L, V deleterious A, G, P, Q, N, G, R,H, K, Q, N, D, E, B5401 preferred F, W, Y, 1°Anchor F, W, Y, L, I, V L,I, V, M, A, L, I, V, M, F, W, Y, A, P, 1°Anchor P M, A, T, I, V, L, M,F, W, Y deleterious G, P, Q, N, D, E, G, D, E, S, T, C, R, H, K, D, E,D, E, Q, N, D, G, E, D, E,

Italicized residues indicate less preferred or “tolerated” residues.

The information in Table II is specific for 9-mers unless otherwisespecified.

Secondary anchor specificities are designated for each positionindependently.

TABLE 5 Expression of Tumor Associated Antigen (TAA) % of TumorsExpressing the TAA TAA Colon Cancer Breast Cancer Lung Cancer CEA 95 5070 P53 50 50 40-60 MAGE 2/3 20-30 20-30 35 HER2/neu 28-50 30-50 20-30Total 99 86-91 91-95

TABLE 6 HLA- Allelle-specific HLA-supertype members supertypeVerified^(a) Predicted^(b) A1 A*0101, A*2501, A*2601, A*2602, A*0102,A*2604, A*3601, A*4301, A*3201, A*2902 A*8001 A2 A*0201, A*0202, A*0203,A*0204, A*0208, A*0210, A*0211, A*0212, A*0205, A*0206, A*0207, A*0209,A*0213 A*0214, A*6802, A*6901 A3 A*0301, A*1101, A*3101, A*3301, A*6801A*0302, A*1102, A*2603, A*3302, A*3303, A*3401, A*3402, A*6601, A*6602,A*7401 A24 A*2301, A*2402, A*3001 A*2403, A*2404, A*3002, A*3003 B7B*0702, B*0703, B*0704, B*0705, B*1508, B*1511, B*4201, B*5901 B*3501,B*3502, B*3503, B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101,B*5102, B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601,B*5602, B*6701, B*7801 B27 B*1401, B*1402, B*1509, B*2702, B*2703,B*2701, B*2707, B*2708, B*3802, B*2704, B*2705, B*2706, B*3801, B*3901,B*3903, B*3904, B*3905, B*4801, B*3902, B*7301 B*4802, B*1510, B*1518,B*1503 B44 B*1801, B*1802, B*3701, B*4402, B*4403, B*4101, B*4501,B*4701, B*4901, B*4404, B*4001, B*4002, B*4006 B*5001 B58 B*5701,B*5702, B*5801, B*5802, B*1516, B*1517 B62 B*1501, B*1502, B*1513,B*5201 B*1301, B*1302, B*1504, B*1505, B*1506, B*1507, B*1515, B*1520,B*1521, B*1512, B*1514, B*1510 ^(a)Verified alleles include alleleswhose specificity has been determined by pool sequencing analysis,peptide binding assays, or by analysis of the sequences of CTL epitopes.^(b)Predicted alleles are alleles whose specificity is predicted on thebasis of B and F pocket structure to overlap with the supertypespecificity.

TABLE 7 Expression of Tumor Associated Antigen (TAA) % of TumorsExpressing the TAA TAA Colon Cancer Breast Cancer Lung Cancer CEA 95 5070 P53 50 50 40-60 MAGE 2/3 20-30 20-30 35 HER2/neu 28-50 30-50 20-30Total 99 86-91 91-95

TABLE 8 Incidence and survival rate of patients with breast, colon, orlung cancer in the United States Estimated 5-Year relative New CasesEstimate survival rates 1998 Deaths 1998 1974-76 1980-82 1986-1993Breast 180,300 43,900 75% 77% 80% Colon 95,600 47,700 50% 56% 63% Lung171,500 160,100 12% 14% 14% Source: Cancer Statistics 1998.January/February 1998, Vol. 48, No. 1

TABLE 9 Population coverage by HLA class I supertype epitopes. MinimalAlleic Frequency Representative HLA Supertype Molecules* Caucasian BlackJapanese Chinese Hispanic Average A2 2.1, 2.2, 2.3, 2.5, 45.8 39.0 42.445.9 43.0 43.2 2.6, 2.7, 68.02 A3 3, 11, 31, 33, 37.5 42.1 45.8 52.743.1 44.2 68.01 B7 7, 51, 53, 35, 54 43.2 55.1 57.1 43.0 49.3 49.5 TotalPopulation 84.3 86.8 89.5 89.8 86.8 87.4 Coverage

TABLE 10 Tumor Associated Antigens and Genes (TAA) ANTIGEN REFERENCEMAGE 1 (Traversari C., Boon T, J. Ex. Med 176: 1453, 1992) MAGE 2 (DeSmet C., Boon T, Immunogenetics, 39(2)121-9, 1994) MAGE 3 (Gaugler B.,Boon T, J. Ex. Med 179: 921, 1994) MAGE-11 (Jurk M., Winnacker L, Int.J. Cancer 75, 762-766, 1998) MAGE-A10 (Huang L., Van Pel A,J.Immunology, 162: 6849-6854) BAGE (Boel P., Bruggen V, Immunity 2: 167,1995) GAGE (Eynde V., Boon T, J. Exp. Med 182: 689, 1995) RAGE (GauglerB., Eynde V, Immunogenetics, 44: 325, 1996) MAGE-C1 (Lucas S., Boon T,Cancer Research, 58, 743-752, 1998) LAGE-1 (Lethel B., Boon T, Int Jcancer, 10; 76(6) 903-908 CAG-3 (Wang R--Rosenberg S, J.Immunology, 161:3591-3596, 1998) DAM (Fleischhauer K., Traversari C, Cancer Research,58, 14, 2969, 1998) MUC1 (Karanikas V., McKenzie IF, J.clnicalinvestigation, 100: 11, 1-10, 1997) MUC2 (Bohm C., Hanski, Int.J.Cancer75, 688-693, 1998) MUC18 (Putz E., Pantel K, Cancer Res 59(1): 241-248,1999) NY-ES0-1 (Chen Y., Old LJ PNAS, 94, 1914-18, 1997) MUM-1 (CoulieP., Boon T, PNAS 92: 7976, 1995) CDK4 (Wolfel T., Beach D, Science 269:1281, 1995) BRCA2 (Wooster R---Stratton M, Nature, 378, 789-791, 1995)NY-LU-1 (Gure A., Chen, Cancer Research, 58, 1034-41, 1998) NY-LU-7(Gure A., Chen, Cancer Research, 58, 1034-41, 1998) NY-LU-12 (Gure A.,Chen, Cancer Research, 58, 1034-41, 1998) CASP8 (Mandruzzato S., BruggenP, J. Ex. Med 186, 5, 785-793, 1997) RAS (Sidransky D., Vogelstein B,Science, 256: 102) KIAA0205 (Gueguen M., Eynde, J.Immunology, 160:6188-94, 1998) SCCs (Molina R., Ballesta AM, Tumor Biol, 17(2): 81-9,1996) p53 (Hollstein M., Harris CC, Science, 253, 49-53, 1991) p73(Kaghad M., Caput D, Cell; 90(4): 809-19, 1997) CEA (Muraro R., SchlomJ, Cancer Research, 45: 5769-55780, 1985) Her 2/neu (Disis M., CheeverM, Cancer Res 54: 1071, 1994) Melan-A (Coulie P., Boon T, J. Ex. Med,180: 35, 1994) gp100 (Bakker A., Figdor, J. Ex. Med 179: 1005, 1994)Tyrosinase (Wolfel T., Boon T, E. J. I 24: 759, 1994) TRP2 (Wang R.,Rosenberg S. A, J. Ex. Med 184: 2207, 1996) gp75/TRP1 (Wang R.,Rosenberg S. A, J. Ex. Med 183: 1131, 1996) PSM (Pinto J. T., Heston W.D. W., Clin Cancer Res 2(9); 1445-1451, 1996) PSA (Correale P., Tsang K,J. Natl cancer institute, 89: 293-300, 1997) PT1-1 (Sun Y., Fisher PB,Cancer Research, 57(1): 18-23, 1997) B-catenin (Robbins P., RosenbergSA, J. Ex. Med 183: 1185, 1996) PRAME (Neumann E., Seliger B, CancerResearch, 58, 4090-4095, 1998) Telomearse (Kishimoto K., Okamoto E, JSurg Oncol, 69(3): 119-124, 1998) FAK (Kornberg LJ, Head Neck, 20(8):745-52, 1998) Tn antigen (Wang Bl, J Submicrosc Cytol Path, 30(4):503-509, 1998) cyclin D1 protein (Linggui K., Yaowu Z, Cancer Lett130(1-2), 93-101, 1998) NOEY2 (Yu Y., Bat RC, PNAS, 96(1): 214-219,1999) EGF-R (Biesterfeld S.---- Cancer Weekly, Feb. 15, 1999) SART-1(Matsumoto H., Itoh K, Japanese Journal of Cancer Research, 59, iss12,1292-1295, 1998) CAPB (Cancer Weekly, Mar. 29, 4-5, 1999) HPVE7(Rosenberg S. A. Immunity, 10, 282-287, 1999) p15 (Rosenberg S. A.,Immunity, 10, 282-287, 1999) Folate receptor (Gruner B. A., Weitman S.D., Investigational New Drugs, Vol16, iss3, 205-219, 1998) CDC27 (WangR. F., Rosenberg SA, Science, vol 284, 1351-1354, 1999) PAGE-1 (Chen, J.Biol. Chem: 273: 17618-17625, 1998) PAGE-4 (Brinkmann: PNAS, 95: 10757,1998) Kallikrein 2 (Darson: Urology, 49: 857-862, 1997) PSCA (Reiter R.,PNAS, 95: 1735-1740, 1998) DD3 (Bussemakers M. J. G, European Urology,35: 408-412, 1999) RBP-1 (Takahashi T., British Journal of Cancer,81(2): 342-349, 1999) RU2 (Eybde V. D., J. Exp. Med, 190 (12):1793-1799, 1999) Folate binding (Kim D., Anticancer Research, 19:2907-2916, 1999) protein EGP-2 (Heidenreich R., Human Gene Therapy, 11:9-19, 2000)

TABLE 11 Tumor-associated antigen (TAA) sequences CEA SEQ ID NO: 11MESPSAPPHRWCIPWQRLLLTASLLTFWNPPTTAKLTIESTPFNVAEGKEVLLLVHNLPQHLFGYSWYKGERVDGNRQIIGYVIGTQQATPGPAYSGREIIYPNASLLIQNIIQNDTGFYTLHVIKSDLVNEEATGQFRVYPELPKPSISSNNSKPVEDKDAVAFTCEPETQDATYLWWVNNQSLPVSPRLQLSNGNRTLTLFNVTRNDTASYKCETQNPVSARRSDSVILNVLYGPDAPTISPLNTSYRSGENLNLSCEAASNPPAQYSWFVNGTFQQSTQELFIPNITVNNSGSYTCQAHNSDTGLNRTTVTTITVYAEPPKPFITSNNSNPVEDEDAVALTCEPEIQNTTYLWWVNNQSLPVSPRLQLSNDNRTLTLLSVTRNDVGPYECGIQNELSVDHSDPVILNVLYGPDDPTISPSYTYYRPGVNLSLSCHAASNPPAQYSWLIDGNIQQHTQELFISNITEKNSGLYTCQANNSASGHSRTTVKTITVSAELPKPSISSNNSKPVEDKDAVAFTCEPEAQNTTYLWWVNGQSLPVSPRLQLSNGNRTLTLFNVTRNDARAYVCGIQNSVSANRSDPVTLDVLYGPDTPIISPPDSSYLSGANLNLSCHSASNPSPQYSWRINGIPQQHTQVLFIAKITPNNNGTYACFVSNLATGRNNSIVKSITVSASGTSPGLSAGATVGIMIGVLVGVA LI Her2/neu SEQ IDNO: 12 MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCGHEQCAAGCTGPKHSDCLACLHFNIISGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGRLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYYMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVEDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLG LDVPV MAGE2 SEQ IDNO: 13 MPLEQRSQHGKPEEGLEARGEALGLVGAQAPATEEQQTASSSSTLVEVTLGEVPAADSPSPPHSPQGASSFSTTINYTLWRQSDEGSSNQEEEGPRMFPDLESEFQAAISRKMVELVHFLLLKYRAREPVTKAEMLESVLRNCQDFFPVIFSKASEYLQLVFGIEVVEVVPISHLYILVTCLGLSYDGLLGDNQVMPKTGLLIIVLAIIAIEGDCAPEEKIWEELSMLEVFEGRRDSVFAHPRKLLMQDLVQENYLEYRQVPGSDPACYEFLWGPRALIETSYVKVLHHTLKIGGEPHIS YPPLHERALREGEE MAGE3SEQ ID NO: 14 MPLEQRSQHCKPEEGLEARGEALGLVGAQAPATEEQEAASSSSTLVEVTLGEVPAAESPDPPQSPQGASSLPTTMNYPLWSQSYEDSSNQEEEGPSTFPDLESEFQAALSRKVAELVIHFLLLKYRAREPVTKAEMLGSVVGNWQYFFPVIFSKASSSLQLVFGIELMEVDPIGHLYIFATCLGLSYDGLLGDNQIMPKAGLLIIVLAIIAREGDCAPEEKIWEELSVLEVFEGREDSILGDPKKLLTQHFVQENYLEYRQVPGSDPACYEFLWGPRALVETSYYKVLHHMVKISGGPHI SYPPLHEWVLREGEE p53SEQ ID NO: 15 MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHECSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDGTTLHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSKLKSKKGQSTSRHKKLMFKTEGPDSD

TABLE 12 Hepatitis B Virus Core Protein (SEQ ID NO: 16)MQLFHLCLIISCSCPTVQASKLCLGWLWGMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTASALYREALESPEHCSPHHTALRQAILCWGELMTLATWVGVNLEDPASRDLVVSYVNTNMGLKFRQLLWFHISCLTFGRETVIEYLVSFGVWIRTPPAYRPPNAPILSTLPETTVVRRRGRSPRRRTPSPRRRRSQSP RRRRSQSRESQC

TABLE 13 HLA-A2 Supertype Family Alleles Prototype Additional AlleleSupertype Alleles HLA-A*0201 HLA-A*0202, A*0203, A*0204, A*0205, A*0206,A*0207, A*6802, A*6901

TABLE 14 List of Vaccine Epitopes No. A2 CTL Response Peptide AllelesWild-type Tumor Reference for Wild-type Epitope Sequence NumberCrossbound¹ Peptide Cell or Analog Epitope Wild-type EpitopesHER-2/neu.689 RLLQETELV 1013.08 2 + + Knutson KL, 2001; Rongeun Y, 1999MAGE-2.157 YLQLVFGIEV 1090.01 4 + + Visseren MJ, 1997; Kawashima I, 1998Fixed-anchor Analogs CEA.24V9 LLTFWNPPV 1243.08 4 + + Kawashima I, 1998HER-2/neu.369V2V9 KVFGSLAFV 1334.10 4 + + Keogh E, 2001 p53.139L2B3KLBPVQLWV² 1323.06 4 + + Keogh E, 2001 p53.149M2 SMPPPGTRV 1295.03 4 + +Keogh E, 2001; Petersen TR, 2001 Heteroclitic Analogs CEA.691H5IMIGHLVGV 1352.02 5 + + Tangri S, 2001 MAGE-3.11215 KVAEIVHFL 1352.035 + + Tangri S,2001 CEA.605D6 YLSGADLNL 1350.01 3 + + Zaremba S, 1997Universal Helper T Cell Epitope PADRE aKXVAAWTLKAAa³ 965.10 Alexander J,1994 ¹All peptides bind to the prototype HLA-A2.1 molecule. ²B indicatesα-aminoisobutyric acid. ³X indicates cyclohexylalanme and a indicatesd-alanine.

TABLE 15 Peptide Solubility Acidic conditions Peptide (pH 2-4)¹ Basicconditions (pH 9.6-13)² DMSO 965.10 + −³ + 1013.08 +/−⁴ + + 1090.01−⁵ + + 1243.08 +⁶ + + 1295.03 + +⁷ + 1323.06 +⁶ + + 1334.10 + − +1350.01 +⁶ + + 1352.02 + − + 1352.03 + +⁷ + ¹0.1% TFA, 0.15-0.1875 Macetic acid, 25 mM pH4 sodium acetate ²25 mM pH 9.6 arginine, 25 mM pH9.6 sodium bicarbonate, 0.1 M NaOH ³Not tested in 0.1 M NaOH, assumedinsoluble since not soluble under other basic conditions ⁴Not soluble inpH 4 acetate buffer ⁵Not tested in diluted acetic acid, assumedinsoluble under these conditions since insoluble under other acidicconditions ⁶Not tested in diluted acetic acid, assumed soluble underthese conditions since soluble in 0.1% TFA ⁷Not tested in 0.1 M NaOH,assumed soluble under these conditions since soluble in other basicbuffers

TABLE 16 Release Specifications of Bulk Drug Substance ComponentPeptides Test Name Test Method Specification Appearance Visual White tooff-white powder Identity Mass spectrometry Molecular Weight Tandem massspectrometry Sequence of peptide Amino acid analysis Amino acidcomposition Purity HPLC ≧90% Acetate Content Ion chromatography Reportresult Peptide content AAA or UV Report results Residual OrganicVolatiles USP 24 <467> Isopropanol ≦300 ppm USP 24 <467> Methylenechloride ≦20 ppm USP 24 <467> Acetonitrile ≦100 ppm Water Content USP 24<921> Report results Endotoxin USP 24 <85> ≦0.5 EU/mg Bioburden USP 24<61> Report results Total Fluorine Combustion/ISE Report results TotalMass Balance Calculation 90-105% NPC + HOAc + H₂O

TABLE 17 Components and Quantitative Composition of EP-2101 Drug ProductComponent Name Concentration (g/L) Peptide  965.10 0.5 1013.08 0.51090.01 0.5 1243.08 0.5 1295.03 0.5 1323.06 0.5 1334.10 0.5 1350.01 0.51352.02 0.5 1352.03 0.5 Adjuvant Montanide ® ISA 51 459 ExcipientsSodium acetate 2.83 Sodium phosphate, dibasic 0.33 DMSO (USP) 50.5

TABLE 18 Components for Use in the Manufacture of EP-2101 Drug ProductComponents for Manufacture of EP-2101 Drug Product Peptides 1352.021295.03 1352.03  965.10 1243.08 1350.01 1013.08 1090.01 1323.06 1334.10Chemicals/Solutions Acetic Acid (USP) NaOH anhydrous (NF) DMSO (USP)Na₂HPO₄•7H₂O (USP) Sterile Water for Injection (USP) AdjuvantMontanide ® ISA 51

TABLE 19 Pool Assignments for EP-2101 Peptide Epitopes Peptide AminoAcid Sequence Solution 1 Solution 2 Solution 3 965.10 AkXVAAWTLKAAa +PADRE® 1013.08 RLLQETELV + 1090.01 YLQLVFGIEV + 1243.08 LLTFWNPPV +1295.03 SMPPPGTRV + 1323.06 KLBPVQLWV + 1334.10 KVFGSLAFV + 1350.01YLSGADLNL + 1352.02 IMIGHLVGV + 1352.03 KVAEIVHFL + + = solutionassignment, a = d-alanine, B = α-aminoisobutyric acid, X= cyclohexylalanine

TABLE 20 Specifications of EP-2101 Bulk Drug Product Test Name TestMethod Specification Endotoxin USP 25 <85> ≦10 EU/ml Sterility USP 25<71> No growth after 14 days

TABLE 21 Specifications of EP-2101 Drug Product Test Name Test MethodSpecification Appearance Visual White to pale yellow emulsion EndotoxinUSP 25 <85> ≦20 EU/ml Sterility USP 25 <71> No growth after 14 days(conforms with 21 CFR 610.12) Viscosity Plate and cone Report value PHpH electrode pH 7.0 ± 1.0 Particle size distribution Laser lightdiffraction Report value Peptide concentration HPLC 0.50 ± 0.25 mg/ml ofemulsion of each peptide Identity HPLC Conforms to standard Extractablevolume Syringe withdrawal ≧1.00 ml Potency In vivo immunogenicityPeptide 1352.02: ≧22 SU and ≦2900 SU Peptide 1334.10: ≧8 SU and ≦3300 SU

TABLE 22 HPLC Parameters for Determination of Peptide Concentration HPLCParameters Mobile Phase A: 0.1% TFA Mobile Phase B: 0.1% TFA in 80%Acetonitrile in water, Column: PLRP-S (300 A, 5 μm, 4.6 × 250 mm),Polymer Laboratories Flow-rate: 1.0 ml/min Wavelength: 214 nm Columntemperature: 40° C. Autosampler temperature: Ambient Solvent GradientTime (min) Flow (ml/min) % A % B Curve  0.00 1.0 95.0 5.0 N/A  5.00 1.080.0 20.0 Linear 40.00 1.0 60.0 40.0 Linear 54.00 1.0 5.0 95.0 Linear60.00 1.0 5.0 95.0 Linear 65.00 1.0 95.0 5.0 Linear 77.00 1.0 95.0 5.0Linear

1. A composition, comprising at least 3 CTL peptides in Table 3 (SEQ IDNOs:2-10).
 2. The composition of claim 1, which comprises at least 4 CTLpeptides in Table 3 (SEQ ID NOs:2-10).
 3. The composition of claim 1,which comprises at least 5 CTL peptides in Table 3 (SEQ ID NOs:2-10). 4.The composition of claim 1, which comprises at least 6 CTL peptides inTable 3 (SEQ ID NOs:2-10).
 5. The composition of claim 1, whichcomprises at least 7 CTL peptides in Table 3 (SEQ ID NOs:2-10).
 6. Thecomposition of claim 1, which comprises at least 8 CTL peptides in Table3 (SEQ ID NOs:2-10).
 7. The composition of claim 1, which comprises all9 CTL peptides in Table 3 (SEQ ID NOs:2-10).
 8. The composition of anyof claims 1-7, which further comprises an HTL peptide.
 9. Thecomposition of claim 8, wherein said HTL peptide comprises SEQ ID NO:1.10. The composition of any of claims 1-9, which further comprises one ormore diluents, different CTL epitopes, different HTL epitopes, carriers,liposomes, an HLA heavy chain, β2-microglobulin, strepavidin,antigen-presenting cell, and/or an adjuvant.
 11. The composition ofclaim 10, which further comprises an adjuvant.
 12. The composition ofclaim 11, wherein said adjuvant is a mineral oil adjuvant.
 13. A methodof delaying the recurrence of cancer following surgery, chemotherapy orradiation comprising administering the composition of any one of claims1-12 to a patient.
 14. The method of claim 13, wherein said cancer isselected from the group consisting of: a. colon cancer; b. non-smallcell lung cancer (NSCLC); c. breast cancer; d. ovarian cancer; and e. acancer of the head and/or neck.